From 5c987974216409990698dcd16b1a42a2e0a16e89 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 8 Oct 2024 12:30:50 +0000 Subject: [PATCH 01/37] Template update for nf-core/tools version 3.0.0 --- .editorconfig | 4 + .github/CONTRIBUTING.md | 10 +- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 23 +- .github/workflows/ci.yml | 17 +- .github/workflows/download_pipeline.yml | 53 ++- .github/workflows/linting.yml | 23 +- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 2 +- .../workflows/template_version_comment.yml | 43 ++ .gitpod.yml | 7 +- .nf-core.yml | 20 +- .pre-commit-config.yaml | 2 +- .prettierignore | 1 + CHANGELOG.md | 2 +- CITATIONS.md | 4 +- README.md | 5 +- assets/multiqc_config.yml | 6 +- assets/schema_input.json | 2 +- conf/base.config | 34 +- conf/igenomes_ignored.config | 9 + conf/modules.config | 1 - conf/test.config | 13 +- docs/images/mqc_fastqc_adapter.png | Bin 23458 -> 0 bytes docs/images/mqc_fastqc_counts.png | Bin 33918 -> 0 bytes docs/images/mqc_fastqc_quality.png | Bin 55769 -> 0 bytes docs/output.md | 11 +- docs/usage.md | 12 +- main.nf | 10 +- modules.json | 12 +- modules/nf-core/fastqc/environment.yml | 2 - modules/nf-core/fastqc/main.nf | 5 +- modules/nf-core/fastqc/meta.yml | 57 +-- modules/nf-core/fastqc/tests/main.nf.test | 225 ++++++++--- .../nf-core/fastqc/tests/main.nf.test.snap | 370 ++++++++++++++++-- modules/nf-core/multiqc/environment.yml | 4 +- modules/nf-core/multiqc/main.nf | 14 +- modules/nf-core/multiqc/meta.yml | 78 ++-- modules/nf-core/multiqc/tests/main.nf.test | 8 + .../nf-core/multiqc/tests/main.nf.test.snap | 20 +- modules/nf-core/multiqc/tests/nextflow.config | 5 + nextflow.config | 148 ++++--- nextflow_schema.json | 85 +--- .../utils_nfcore_demultiplex_pipeline/main.nf | 56 +-- .../nf-core/utils_nextflow_pipeline/main.nf | 24 +- .../tests/nextflow.config | 2 +- .../nf-core/utils_nfcore_pipeline/main.nf | 45 ++- .../nf-core/utils_nfschema_plugin/main.nf | 46 +++ .../nf-core/utils_nfschema_plugin/meta.yml | 35 ++ .../utils_nfschema_plugin/tests/main.nf.test | 117 ++++++ .../tests/nextflow.config | 8 + .../tests/nextflow_schema.json | 8 +- .../nf-core/utils_nfvalidation_plugin/main.nf | 62 --- .../utils_nfvalidation_plugin/meta.yml | 44 --- .../tests/main.nf.test | 200 ---------- .../utils_nfvalidation_plugin/tests/tags.yml | 2 - workflows/demultiplex.nf | 23 +- 57 files changed, 1211 insertions(+), 812 deletions(-) create mode 100644 .github/workflows/template_version_comment.yml create mode 100644 conf/igenomes_ignored.config delete mode 100755 docs/images/mqc_fastqc_adapter.png delete mode 100755 docs/images/mqc_fastqc_counts.png delete mode 100755 docs/images/mqc_fastqc_quality.png create mode 100644 modules/nf-core/multiqc/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config rename subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%) delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/.editorconfig b/.editorconfig index 72dda289..e1058815 100644 --- a/.editorconfig +++ b/.editorconfig @@ -11,6 +11,7 @@ indent_style = space [*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 + # These files are edited and tested upstream in nf-core/modules [/modules/nf-core/**] charset = unset @@ -25,9 +26,12 @@ insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset + + [/assets/email*] indent_size = unset + # ignore python and markdown [*.{py,md}] indent_style = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index a16dcd60..a0db51e0 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/demultiplex, the standard workflow 1. Check that there isn't already an issue about your idea in the [nf-core/demultiplex issues](https://github.com/nf-core/demultiplex/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/demultiplex repository](https://github.com/nf-core/demultiplex) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). +4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). @@ -40,7 +40,7 @@ There are typically two types of tests that run: ### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. +To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. @@ -75,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards: 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. @@ -86,7 +86,7 @@ If you wish to contribute a new step, please use the following coding standards: Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. +Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. ### Default processes resource requirements @@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g ### Nextflow version bumping -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` +If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` ### Images and figures diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index d7bbf615..b47515e4 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/demu - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/demultiplex/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/demultiplex _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. -- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index f5d63182..34b0d112 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,18 +1,33 @@ name: nf-core AWS full size tests -# This workflow is triggered on published releases. +# This workflow is triggered on PRs opened against the master branch. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: - release: - types: [published] + pull_request: + branches: + - master workflow_dispatch: + pull_request_review: + types: [submitted] + jobs: run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/demultiplex' + if: github.repository == 'nf-core/demultiplex' && github.event.review.state == 'approved' runs-on: ubuntu-latest steps: + - uses: octokit/request-action@v2.x + id: check_approvals + with: + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + - id: test_variables + run: | + JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' + CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') + test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6c2ba453..ae05ff11 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,6 +7,7 @@ on: pull_request: release: types: [published] + workflow_dispatch: env: NXF_ANSI_LOG: false @@ -24,7 +25,7 @@ jobs: strategy: matrix: NXF_VER: - - "23.04.0" + - "24.04.2" - "latest-everything" steps: - name: Check out pipeline code @@ -38,9 +39,21 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data + - name: Run pipeline with test data (docker) # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + + - name: Run pipeline with test data (singularity) + # TODO nf-core: You can customise CI pipeline run tests as required + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results + if: "${{ github.base_ref == 'master' }}" + + - name: Run pipeline with test data (conda) + # TODO nf-core: You can customise CI pipeline run tests as required + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results + if: "${{ github.base_ref == 'master' }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2d20d644..713dc3e7 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -1,4 +1,4 @@ -name: Test successful pipeline download with 'nf-core download' +name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually @@ -8,7 +8,7 @@ on: workflow_dispatch: inputs: testbranch: - description: "The specific branch you wish to utilize for the test execution of nf-core download." + description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." required: true default: "dev" pull_request: @@ -39,9 +39,11 @@ jobs: with: python-version: "3.12" architecture: "x64" - - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 with: - singularity-version: 3.8.3 + apptainer-version: 1.3.4 - name: Install dependencies run: | @@ -54,33 +56,64 @@ jobs: echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + - name: Make a cache directory for the container images + run: | + mkdir -p ./singularity_container_images + - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ + nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ --container-cache-utilisation 'amend' \ - --download-configuration + --download-configuration 'yes' - name: Inspect download run: tree ./${{ env.REPOTITLE_LOWERCASE }} + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} + - name: Run the downloaded pipeline (stub) id: stub_run_pipeline continue-on-error: true env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline if: ${{ job.steps.stub_run_pipeline.status == failure() }} env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} + + - name: Compare container image counts + run: | + if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ env.IMAGE_COUNT_INITIAL }} + final_count=${{ env.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 1fcafe88..b882838a 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,6 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: push: @@ -41,17 +41,32 @@ jobs: python-version: "3.12" architecture: "x64" + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.0.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yaml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Run nf-core pipelines lint + if: ${{ github.base_ref != 'master' }} + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - - name: Run nf-core lint + - name: Run nf-core pipelines lint --release + if: ${{ github.base_ref == 'master' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 40acc23f..42e519bf 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 + uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 03ecfcf7..c6ba35df 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml new file mode 100644 index 00000000..9dea41f0 --- /dev/null +++ b/.github/workflows/template_version_comment.yml @@ -0,0 +1,43 @@ +name: nf-core template version comment +# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. +# It posts a comment to the PR, even if it comes from a fork. + +on: pull_request_target + +jobs: + template_version: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + + - name: Read template version from .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.0.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install nf-core + run: | + python -m pip install --upgrade pip + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Check nf-core outdated + id: nf_core_outdated + run: pip list --outdated | grep nf-core + + - name: Post nf-core template version comment + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + if: | + ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core' + with: + repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} + allow-repeats: false + message: | + ## :warning: Newer version of the nf-core template is available. + + Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + Please update your pipeline to the latest version. + + For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + # diff --git a/.gitpod.yml b/.gitpod.yml index 105a1821..46118637 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,17 +4,14 @@ tasks: command: | pre-commit install --install-hooks nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - unset JAVA_TOOL_OPTIONS vscode: extensions: # based on nf-core.nf-core-extensionpack - - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code + #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code - charliermarsh.ruff # Code linter Ruff diff --git a/.nf-core.yml b/.nf-core.yml index e0b85a77..43121c49 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,2 +1,20 @@ +bump_version: null +lint: + actions_ci: false + files_unchanged: + - .github/ISSUE_TEMPLATE/bug_report.yml + - .github/workflows/linting.yml +nf_core_version: 3.0.0 +org_path: null repository_type: pipeline -nf_core_version: "2.14.1" +template: + author: Chelsea Sawyer, Edmund Miller, Matthias De Smet + description: Demultiplexing pipeline for Illumina sequencing data + force: false + is_nfcore: true + name: demultiplex + org: nf-core + outdir: . + skip_features: null + version: 1.5.2 +update: null diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4dc0f1dc..9e9f0e1c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - prettier@3.2.5 - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "2.7.3" + rev: "3.0.3" hooks: - id: editorconfig-checker alias: ec diff --git a/.prettierignore b/.prettierignore index 437d763d..610e5069 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,3 +1,4 @@ + email_template.html adaptivecard.json slackreport.json diff --git a/CHANGELOG.md b/CHANGELOG.md index cc1302f2..76b6e06c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.4.1 - [date] +## v1.5.2 - [date] Initial release of nf-core/demultiplex, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index 4f483439..db8f8fda 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,11 +12,11 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools diff --git a/README.md b/README.md index 2cfd9587..a48514f5 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ [![GitHub Actions Linting Status](https://github.com/nf-core/demultiplex/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demultiplex/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/demultiplex/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -67,8 +67,7 @@ nextflow run nf-core/demultiplex \ ``` > [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; -> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/demultiplex/usage) and the [parameter documentation](https://nf-co.re/demultiplex/parameters). diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f970dd1a..36486271 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,9 +1,7 @@ report_comment: > - - This report has been generated by the nf-core/demultiplex + This report has been generated by the nf-core/demultiplex analysis pipeline. For information about how to interpret these results, please see the - documentation. - + documentation. report_section_order: "nf-core-demultiplex-methods-description": order: -1000 diff --git a/assets/schema_input.json b/assets/schema_input.json index 0e9f6c27..cf43c8f9 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/demultiplex/master/assets/schema_input.json", "title": "nf-core/demultiplex pipeline - params.input schema", "description": "Schema for the file provided with params.input", diff --git a/conf/base.config b/conf/base.config index 66ba4854..23d1f6be 100644 --- a/conf/base.config +++ b/conf/base.config @@ -11,9 +11,9 @@ process { // TODO nf-core: Check the defaults for all processes - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 @@ -27,30 +27,30 @@ process { // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config new file mode 100644 index 00000000..b4034d82 --- /dev/null +++ b/conf/igenomes_ignored.config @@ -0,0 +1,9 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for iGenomes paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Empty genomes dictionary to use when igenomes is ignored. +---------------------------------------------------------------------------------------- +*/ + +params.genomes = [:] diff --git a/conf/modules.config b/conf/modules.config index d203d2b6..d266a387 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -21,7 +21,6 @@ process { withName: FASTQC { ext.args = '--quiet' } - withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/conf/test.config b/conf/test.config index 24a18382..1db39e39 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,15 +10,18 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 100755 index 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zXwhtT%ei{n#FzEH|C;yZ>+$!u_x#*+`=L8{b9SH^9&27u3G_Gxqxe`L2UJtdxghk z&-wzDFvLvW{chK5u3{n6GSKKy!P&C6w^IFpbD0bcp^A{{2lcLh_DXj@ybtYvc^;(2 M)78&qol`;+0Fu7JivR!s diff --git a/docs/output.md b/docs/output.md index 5586f3eb..a4cba9ae 100644 --- a/docs/output.md +++ b/docs/output.md @@ -14,6 +14,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [FastQC](#fastqc) - Raw read QC - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline + - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC @@ -29,16 +30,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). -![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) - -![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) - -![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) - -:::note -The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. -::: - ### MultiQC
diff --git a/docs/usage.md b/docs/usage.md index 171de78f..bfac79c2 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -85,9 +85,9 @@ The above pipeline run specified with a params file in yaml format: nextflow run nf-core/demultiplex -profile docker -params-file params.yaml ``` -with `params.yaml` containing: +with: -```yaml +```yaml title="params.yaml" input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' @@ -199,14 +199,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). -## Azure Resource Requests - -To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. -We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. - -Note that the choice of VM size depends on your quota and the overall workload during the analysis. -For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). - ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. diff --git a/main.nf b/main.nf index 58725ac4..c91a0de0 100644 --- a/main.nf +++ b/main.nf @@ -9,8 +9,6 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS @@ -20,7 +18,6 @@ nextflow.enable.dsl = 2 include { DEMULTIPLEX } from './workflows/demultiplex' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_demultiplex_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_demultiplex_pipeline' - include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_demultiplex_pipeline' /* @@ -56,10 +53,8 @@ workflow NFCORE_DEMULTIPLEX { DEMULTIPLEX ( samplesheet ) - emit: multiqc_report = DEMULTIPLEX.out.multiqc_report // channel: /path/to/multiqc_report.html - } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -70,27 +65,24 @@ workflow NFCORE_DEMULTIPLEX { workflow { main: - // // SUBWORKFLOW: Run initialisation tasks // PIPELINE_INITIALISATION ( params.version, - params.help, params.validate_params, params.monochrome_logs, args, params.outdir, params.input ) - + // // WORKFLOW: Run main workflow // NFCORE_DEMULTIPLEX ( PIPELINE_INITIALISATION.out.samplesheet ) - // // SUBWORKFLOW: Run completion tasks // diff --git a/modules.json b/modules.json index efbc9215..b009af98 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] } } @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", + "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", "installed_by": ["subworkflows"] }, - "utils_nfvalidation_plugin": { + "utils_nfschema_plugin": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a..691d4c76 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,5 @@ -name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d79f1c86..d8989f48 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -26,7 +26,10 @@ process FASTQC { def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) + // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 + // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index ee5507e0..4827da7a 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -16,35 +16,44 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] + identifier: biotools:fastqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 70edae4d..e9d79a07 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -23,17 +23,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -54,16 +51,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -83,13 +78,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -109,13 +102,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -138,22 +129,20 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -173,21 +162,18 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } test("sarscov2 single-end [fastq] - stub") { - options "-stub" - + options "-stub" when { process { """ @@ -201,12 +187,123 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } + { assert process.success }, + { assert snapshot(process.out).match() } ) } } + test("sarscov2 paired-end [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 interleaved [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 paired-end [bam] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 multiple [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 custom_prefix - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 86f7c311..d5db3092 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,88 +1,392 @@ { - "fastqc_versions_interleaved": { + "sarscov2 custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:07.293713" + "timestamp": "2024-07-22T11:02:16.374038" }, - "fastqc_stub": { + "sarscov2 single-end [fastq] - stub": { "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:24.993809" + }, + "sarscov2 custom_prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:31:01.425198" + "timestamp": "2024-07-22T11:03:10.93942" }, - "fastqc_versions_multiple": { + "sarscov2 interleaved [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:55.797907" + "timestamp": "2024-07-22T11:01:42.355718" }, - "fastqc_versions_bam": { + "sarscov2 paired-end [bam]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:26.795862" + "timestamp": "2024-07-22T11:01:53.276274" }, - "fastqc_versions_single": { + "sarscov2 multiple [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:27.043675" + "timestamp": "2024-07-22T11:02:05.527626" }, - "fastqc_versions_paired": { + "sarscov2 paired-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:31.188871" + }, + "sarscov2 paired-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:34.273566" + }, + "sarscov2 multiple [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:47.584191" + "timestamp": "2024-07-22T11:03:02.304411" }, - "fastqc_versions_custom_prefix": { + "sarscov2 single-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:19.095607" + }, + "sarscov2 interleaved [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:44.640184" + }, + "sarscov2 paired-end [bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:41:14.576531" + "timestamp": "2024-07-22T11:02:53.550742" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67..f1cd99b0 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.24.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352f..b9ccebdb 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -23,16 +25,22 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc35..b16c1879 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -12,40 +13,59 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242e..33316a7d 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -8,6 +8,8 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { @@ -17,6 +19,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +45,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +72,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd802..b779e469 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-07-10T12:41:34.562023" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-07-10T11:27:11.933869532" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-07-10T11:26:56.709849369" } -} \ No newline at end of file +} diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 00000000..c537a6a3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + } +} diff --git a/nextflow.config b/nextflow.config index d6db8059..9b53aeb3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,7 +16,6 @@ params { genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - // MultiQC options multiqc_config = null multiqc_title = null @@ -33,48 +32,26 @@ params { monochrome_logs = false hook_url = null help = false + help_full = false + show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - // Config options config_profile_name = null config_profile_description = null + custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - - // Max resource options - // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' - // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' - validationShowHiddenParams = false - validate_params = true - + validate_params = true + } // Load base.config by default for all pipelines includeConfig 'conf/base.config' -// Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} - -// Load nf-core/demultiplex custom profiles from different institutions. -try { - includeConfig "${params.custom_config_base}/pipeline/demultiplex.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/demultiplex profiles: ${params.custom_config_base}/pipeline/demultiplex.config") -} profiles { debug { dumpHashes = true @@ -89,7 +66,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false - conda.channels = ['conda-forge', 'bioconda', 'defaults'] + conda.channels = ['conda-forge', 'bioconda'] apptainer.enabled = false } mamba { @@ -178,25 +155,23 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } -// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled -// Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' +// Load nf-core custom profiles from different Institutions +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" -// Nextflow plugins -plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} +// Load nf-core/demultiplex custom profiles from different institutions. +// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs +// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/demultiplex.config" : "/dev/null" +// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' +charliecloud.registry = 'quay.io' // Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' -} else { - params.genomes = [:] -} +includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -208,8 +183,15 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" } -// Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set bash options +process.shell = """\ +bash + +set -e # Exit if a tool returns a non-zero status/exit code +set -u # Treat unset variables and parameters as an error +set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute +set -C # No clobber - prevent output redirection from overwriting files. +""" // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false @@ -238,43 +220,47 @@ manifest { homePage = 'https://github.com/nf-core/demultiplex' description = """Demultiplexing pipeline for Illumina sequencing data""" mainScript = 'main.nf' - nextflowVersion = '!>=23.04.0' - version = '1.4.1' + nextflowVersion = '!>=24.04.2' + version = '1.5.2' doi = '' } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' +// Nextflow plugins +plugins { + id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} + +validation { + defaultIgnoreParams = ["genomes"] + help { + enabled = true + command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + fullParameter = "help_full" + showHiddenParameter = "show_hidden" + beforeText = """ +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m +\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m + \033[0;32m`._,._,\'\033[0m +\033[0;35m ${manifest.name} ${manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- +""" + afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } +* Software dependencies + https://github.com/${manifest.name}/blob/master/CITATIONS.md +""" + } + summary { + beforeText = validation.help.beforeText + afterText = validation.help.afterText } } + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' + diff --git a/nextflow_schema.json b/nextflow_schema.json index 9238b3b3..cbc7aca8 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/demultiplex/master/nextflow_schema.json", "title": "nf-core/demultiplex pipeline parameters", "description": "Demultiplexing pipeline for Illumina sequencing data", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -71,6 +71,14 @@ "fa_icon": "fas fa-ban", "hidden": true, "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." + }, + "igenomes_base": { + "type": "string", + "format": "directory-path", + "description": "The base path to the igenomes reference files", + "fa_icon": "fas fa-ban", + "hidden": true, + "default": "s3://ngi-igenomes/igenomes/" } } }, @@ -122,41 +130,6 @@ } } }, - "max_job_request_options": { - "title": "Max job request options", - "type": "object", - "fa_icon": "fab fa-acquisitions-incorporated", - "description": "Set the top limit for requested resources for any single job.", - "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", - "properties": { - "max_cpus": { - "type": "integer", - "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, - "fa_icon": "fas fa-microchip", - "hidden": true, - "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" - }, - "max_memory": { - "type": "string", - "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", - "fa_icon": "fas fa-memory", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "hidden": true, - "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" - }, - "max_time": { - "type": "string", - "description": "Maximum amount of time that can be requested for any single job.", - "default": "240.h", - "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", - "hidden": true, - "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" - } - } - }, "generic_options": { "title": "Generic options", "type": "object", @@ -164,12 +137,6 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, "version": { "type": "boolean", "description": "Display version and exit.", @@ -245,27 +212,6 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "validationShowHiddenParams": { - "type": "boolean", - "fa_icon": "far fa-eye-slash", - "description": "Show all params when using `--help`", - "hidden": true, - "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "validationFailUnrecognisedParams": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters fails when an unrecognised parameter is found.", - "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." - }, - "validationLenientMode": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters in lenient more.", - "hidden": true, - "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." - }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", @@ -278,19 +224,16 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" - }, - { - "$ref": "#/definitions/reference_genome_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/institutional_config_options" + "$ref": "#/$defs/reference_genome_options" }, { - "$ref": "#/definitions/max_job_request_options" + "$ref": "#/$defs/institutional_config_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf index 12f7eb1a..3c22b0f6 100644 --- a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf @@ -8,17 +8,14 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' -include { paramsSummaryMap } from 'plugin/nf-validation' -include { fromSamplesheet } from 'plugin/nf-validation' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' -include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* ======================================================================================== @@ -30,7 +27,6 @@ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit - help // boolean: Display help text validate_params // boolean: Boolean whether to validate parameters against the schema at runtime monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args @@ -51,20 +47,16 @@ workflow PIPELINE_INITIALISATION { workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 ) + // // Validate parameters and generate parameter summary to stdout // - pre_help_text = nfCoreLogo(monochrome_logs) - post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) - def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " - UTILS_NFVALIDATION_PLUGIN ( - help, - workflow_command, - pre_help_text, - post_help_text, + UTILS_NFSCHEMA_PLUGIN ( + workflow, validate_params, - "nextflow_schema.json" + null ) + // // Check config provided to the pipeline @@ -80,8 +72,9 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // + Channel - .fromSamplesheet("input") + .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { @@ -91,8 +84,8 @@ workflow PIPELINE_INITIALISATION { } } .groupTuple() - .map { - validateInputSamplesheet(it) + .map { samplesheet -> + validateInputSamplesheet(samplesheet) } .map { meta, fastqs -> @@ -117,13 +110,13 @@ workflow PIPELINE_COMPLETION { email // string: email address email_on_fail // string: email address sent on pipeline failure plaintext_email // boolean: Send plain-text email instead of HTML + outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output hook_url // string: hook URL for notifications multiqc_report // string: Path to MultiQC report main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") // @@ -131,11 +124,18 @@ workflow PIPELINE_COMPLETION { // workflow.onComplete { if (email || email_on_fail) { - completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + completionEmail( + summary_params, + email, + email_on_fail, + plaintext_email, + outdir, + monochrome_logs, + multiqc_report.toList() + ) } completionSummary(monochrome_logs) - if (hook_url) { imNotification(summary_params, hook_url) } @@ -165,7 +165,7 @@ def validateInputSamplesheet(input) { def (metas, fastqs) = input[1..2] // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1 if (!endedness_ok) { error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") } @@ -197,7 +197,6 @@ def genomeExistsError() { error(error_string) } } - // // Generate methods description for MultiQC // @@ -239,8 +238,10 @@ def methodsDescriptionText(mqc_methods_yaml) { // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list def temp_doi_ref = "" - String[] manifest_doi = meta.manifest_map.doi.tokenize(",") - for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + def manifest_doi = meta.manifest_map.doi.tokenize(",") + manifest_doi.each { doi_ref -> + temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + } meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) } else meta["doi_text"] = "" meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " @@ -261,3 +262,4 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } + diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index ac31f28f..28e32b20 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -2,10 +2,6 @@ // Subworkflow with functionality that may be useful for any Nextflow pipeline // -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - /* ======================================================================================== SUBWORKFLOW DEFINITION @@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Generate version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) { def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') def filename = "params_${timestamp}.json" def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() } @@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) { // When running with -profile conda, warn if channels have not been set-up appropriately // def checkCondaChannels() { - Yaml parser = new Yaml() + def parser = new org.yaml.snakeyaml.Yaml() def channels = [] try { def config = parser.load("conda config --show channels".execute().text) @@ -102,14 +98,16 @@ def checkCondaChannels() { // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def required_channels_in_order = ['conda-forge', 'bioconda'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + + required_channels_in_order.eachWithIndex { channel, index -> + if (index < required_channels_in_order.size() - 1) { + channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1])) + } } if (channels_missing | channel_priority_violation) { diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index d0a926bf..a09572e5 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 14558c39..cbd8495b 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -2,9 +2,6 @@ // Subworkflow with utility functions specific to the nf-core pipeline template // -import org.yaml.snakeyaml.Yaml -import nextflow.extension.FilesEx - /* ======================================================================================== SUBWORKFLOW DEFINITION @@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE { // Warn if a -profile or Nextflow config has not been provided to run the pipeline // def checkConfigProvided() { - valid_config = true + def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + @@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) { // def workflowCitation() { def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") + def manifest_doi = workflow.manifest.doi.tokenize(",") // Using a loop to handle multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + manifest_doi.each { doi_ref -> + temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + } return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + @@ -84,7 +83,7 @@ def workflowCitation() { // Generate workflow version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -102,8 +101,8 @@ def getWorkflowVersion() { // Get software versions for pipeline // def processVersionsFromYAML(yaml_file) { - Yaml yaml = new Yaml() - versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } return yaml.dumpAsMap(versions).trim() } @@ -124,7 +123,7 @@ def workflowVersionToYAML() { def softwareVersionsToYAML(ch_versions) { return ch_versions .unique() - .map { processVersionsFromYAML(it) } + .map { version -> processVersionsFromYAML(version) } .unique() .mix(Channel.of(workflowVersionToYAML())) } @@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - for (group in summary_params.keySet()) { + summary_params.keySet().each { group -> def group_params = summary_params.get(group) // This gets the parameters of that particular group if (group_params) { summary_section += "

    $group

    \n" summary_section += "
    \n" - for (param in group_params.keySet()) { + group_params.keySet().sort().each { param -> summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" } summary_section += "
    \n" } } - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" @@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) { // nf-core logo // def nfCoreLogo(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map String.format( """\n ${dashedLine(monochrome_logs)} @@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) { // Return dashed line // def dashedLine(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map return "-${colors.dim}----------------------------------------------------${colors.reset}-" } @@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) { // ANSII colours used for terminal logging // def logColours(monochrome_logs=true) { - Map colorcodes = [:] + def colorcodes = [:] as Map // Reset / Meta colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" @@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi } def summary = [:] - for (group in summary_params.keySet()) { + summary_params.keySet().sort().each { group -> summary << summary_params[group] } @@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def sendmail_html = sendmail_template.toString() // Send the HTML e-mail - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } @@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); output_tf.delete() } @@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Print pipeline summary on completion // def completionSummary(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" @@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - for (group in summary_params.keySet()) { + summary_params.keySet().sort().each { group -> summary << summary_params[group] } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 00000000..4994303e --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,46 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + + main: + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + if(parameters_schema) { + log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) + } else { + log.info paramsSummaryLog(input_workflow) + } + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + if(parameters_schema) { + validateParameters(parameters_schema:parameters_schema) + } else { + validateParameters() + } + } + + emit: + dummy_emit = true +} + diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 00000000..f7d9f028 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,35 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 00000000..842dc432 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 00000000..0907ac58 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.1.0" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json similarity index 95% rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json index 7626c1c9..331e0d2f 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -87,10 +87,10 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf deleted file mode 100644 index 2585b65d..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ /dev/null @@ -1,62 +0,0 @@ -// -// Subworkflow that uses the nf-validation plugin to render help text and parameter summary -// - -/* -======================================================================================== - IMPORT NF-VALIDATION PLUGIN -======================================================================================== -*/ - -include { paramsHelp } from 'plugin/nf-validation' -include { paramsSummaryLog } from 'plugin/nf-validation' -include { validateParameters } from 'plugin/nf-validation' - -/* -======================================================================================== - SUBWORKFLOW DEFINITION -======================================================================================== -*/ - -workflow UTILS_NFVALIDATION_PLUGIN { - - take: - print_help // boolean: print help - workflow_command // string: default commmand used to run pipeline - pre_help_text // string: string to be printed before help text and summary log - post_help_text // string: string to be printed after help text and summary log - validate_params // boolean: validate parameters - schema_filename // path: JSON schema file, null to use default value - - main: - - log.debug "Using schema file: ${schema_filename}" - - // Default values for strings - pre_help_text = pre_help_text ?: '' - post_help_text = post_help_text ?: '' - workflow_command = workflow_command ?: '' - - // - // Print help message if needed - // - if (print_help) { - log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text - System.exit(0) - } - - // - // Print parameter summary to stdout - // - log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text - - // - // Validate parameters relative to the parameter JSON schema - // - if (validate_params){ - validateParameters(parameters_schema: schema_filename) - } - - emit: - dummy_emit = true -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml deleted file mode 100644 index 3d4a6b04..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NFVALIDATION_PLUGIN" -description: Use nf-validation to initiate and validate a pipeline -keywords: - - utility - - pipeline - - initialise - - validation -components: [] -input: - - print_help: - type: boolean - description: | - Print help message and exit - - workflow_command: - type: string - description: | - The command to run the workflow e.g. "nextflow run main.nf" - - pre_help_text: - type: string - description: | - Text to print before the help message - - post_help_text: - type: string - description: | - Text to print after the help message - - validate_params: - type: boolean - description: | - Validate the parameters and error if invalid. - - schema_filename: - type: string - description: | - The filename of the schema to validate against. -output: - - dummy_emit: - type: boolean - description: | - Dummy emit to make nf-core subworkflows lint happy -authors: - - "@adamrtalbot" -maintainers: - - "@adamrtalbot" - - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test deleted file mode 100644 index 5784a33f..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ /dev/null @@ -1,200 +0,0 @@ -nextflow_workflow { - - name "Test Workflow UTILS_NFVALIDATION_PLUGIN" - script "../main.nf" - workflow "UTILS_NFVALIDATION_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "plugin/nf-validation" - tag "'plugin/nf-validation'" - tag "utils_nfvalidation_plugin" - tag "subworkflows/utils_nfvalidation_plugin" - - test("Should run nothing") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should run help") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with command") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with extra text") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = "pre-help-text" - post_help_text = "post-help-text" - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('pre-help-text') } }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } }, - { assert workflow.stdout.any { it.contains('post-help-text') } } - ) - } - } - - test("Should validate params") { - - when { - - params { - monochrome_logs = true - test_data = '' - outdir = 1 - } - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = true - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } - ) - } - } -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml deleted file mode 100644 index 60b1cfff..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfvalidation_plugin: - - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/demultiplex.nf b/workflows/demultiplex.nf index b7a828e9..e865b30a 100644 --- a/workflows/demultiplex.nf +++ b/workflows/demultiplex.nf @@ -3,10 +3,9 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - include { FASTQC } from '../modules/nf-core/fastqc/main' include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMap } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_demultiplex_pipeline' @@ -21,12 +20,10 @@ workflow DEMULTIPLEX { take: ch_samplesheet // channel: samplesheet read in from --input - main: ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() - // // MODULE: Run FastQC // @@ -42,11 +39,12 @@ workflow DEMULTIPLEX { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_pipeline_software_mqc_versions.yml', + name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } + // // MODULE: MultiQC // @@ -59,18 +57,19 @@ workflow DEMULTIPLEX { Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - + ch_multiqc_files = ch_multiqc_files.mix( + ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) ch_methods_description = Channel.value( methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) ch_multiqc_files = ch_multiqc_files.mix( ch_methods_description.collectFile( @@ -83,12 +82,14 @@ workflow DEMULTIPLEX { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [] ) - emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] + } /* From 96e2f07f27857fdbd598c2c99620579e261a819b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 9 Oct 2024 11:04:24 +0000 Subject: [PATCH 02/37] Template update for nf-core/tools version 3.0.1 --- .editorconfig | 4 - .github/CONTRIBUTING.md | 2 +- .github/workflows/awsfulltest.yml | 6 +- .github/workflows/linting.yml | 4 +- .nf-core.yml | 2 +- .prettierignore | 1 - docs/output.md | 1 - modules.json | 6 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- .../nf-core/multiqc/tests/main.nf.test.snap | 26 +- nextflow.config | 8 +- .../utils_nfcore_demultiplex_pipeline/main.nf | 12 +- .../nf-core/utils_nextflow_pipeline/main.nf | 46 ++- .../nf-core/utils_nfcore_pipeline/main.nf | 279 ++++++++++-------- 15 files changed, 209 insertions(+), 194 deletions(-) diff --git a/.editorconfig b/.editorconfig index e1058815..72dda289 100644 --- a/.editorconfig +++ b/.editorconfig @@ -11,7 +11,6 @@ indent_style = space [*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 - # These files are edited and tested upstream in nf-core/modules [/modules/nf-core/**] charset = unset @@ -26,12 +25,9 @@ insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset - - [/assets/email*] indent_size = unset - # ignore python and markdown [*.{py,md}] indent_style = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index a0db51e0..40b91d2c 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -90,7 +90,7 @@ Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json ### Default processes resource requirements -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. +Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 34b0d112..8e4df67f 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,16 +14,18 @@ on: jobs: run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/demultiplex' && github.event.review.state == 'approved' + # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered + if: github.repository == 'nf-core/demultiplex' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest steps: - uses: octokit/request-action@v2.x id: check_approvals with: - route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - id: test_variables + if: github.event_name != 'workflow_dispatch' run: | JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index b882838a..a502573c 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -42,10 +42,10 @@ jobs: architecture: "x64" - name: read .nf-core.yml - uses: pietrobolcato/action-read-yaml@1.0.0 + uses: pietrobolcato/action-read-yaml@1.1.0 id: read_yml with: - config: ${{ github.workspace }}/.nf-core.yaml + config: ${{ github.workspace }}/.nf-core.yml - name: Install dependencies run: | diff --git a/.nf-core.yml b/.nf-core.yml index 43121c49..de3b862f 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -4,7 +4,7 @@ lint: files_unchanged: - .github/ISSUE_TEMPLATE/bug_report.yml - .github/workflows/linting.yml -nf_core_version: 3.0.0 +nf_core_version: 3.0.1 org_path: null repository_type: pipeline template: diff --git a/.prettierignore b/.prettierignore index 610e5069..437d763d 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,4 +1,3 @@ - email_template.html adaptivecard.json slackreport.json diff --git a/docs/output.md b/docs/output.md index a4cba9ae..8824dbf1 100644 --- a/docs/output.md +++ b/docs/output.md @@ -14,7 +14,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [FastQC](#fastqc) - Raw read QC - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC diff --git a/modules.json b/modules.json index b009af98..bcd1026f 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c", "installed_by": ["modules"] } } @@ -21,12 +21,12 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", + "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", + "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index f1cd99b0..6f5b867b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.24.1 + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index b9ccebdb..9724d2f3 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index b779e469..2fcbb5ff 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T12:41:34.562023" + "timestamp": "2024-10-02T17:51:46.317523" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T11:27:11.933869532" + "timestamp": "2024-10-02T17:52:20.680978" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T11:26:56.709849369" + "timestamp": "2024-10-02T17:52:09.185842" } -} +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 9b53aeb3..2979d348 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,10 +12,12 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false + // MultiQC options multiqc_config = null multiqc_title = null @@ -36,6 +38,7 @@ params { show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' + // Config options config_profile_name = null config_profile_description = null @@ -44,9 +47,9 @@ params { custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null + // Schema validation default options validate_params = true - } // Load base.config by default for all pipelines @@ -161,6 +164,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa // Load nf-core/demultiplex custom profiles from different institutions. // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/demultiplex.config" : "/dev/null" + // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled // Set to your registry if you have a mirror of containers @@ -172,6 +176,7 @@ charliecloud.registry = 'quay.io' // Load igenomes.config if required includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -263,4 +268,3 @@ validation { // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' - diff --git a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf index 3c22b0f6..8e2744f7 100644 --- a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf @@ -18,9 +18,9 @@ include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW TO INITIALISE PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_INITIALISATION { @@ -99,9 +99,9 @@ workflow PIPELINE_INITIALISATION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW FOR PIPELINE COMPLETION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_COMPLETION { @@ -147,9 +147,9 @@ workflow PIPELINE_COMPLETION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Check and validate pipeline parameters diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 28e32b20..2b0dc67a 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,13 +3,12 @@ // /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { - take: print_version // boolean: print version dump_parameters // boolean: dump parameters @@ -22,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Print workflow version and exit on --version // if (print_version) { - log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + log.info("${workflow.manifest.name} ${getWorkflowVersion()}") System.exit(0) } @@ -45,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -72,11 +71,11 @@ def getWorkflowVersion() { // Dump pipeline parameters to a JSON file // def dumpParametersToJSON(outdir) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = groovy.json.JsonOutput.toJson(params) - temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) + def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() @@ -91,9 +90,14 @@ def checkCondaChannels() { try { def config = parser.load("conda config --show channels".execute().text) channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return + } + catch (NullPointerException e) { + log.warn("Could not verify conda channel configuration.") + return null + } + catch (IOException e) { + log.warn("Could not verify conda channel configuration.") + return null } // Check that all channels are present @@ -106,19 +110,13 @@ def checkCondaChannels() { required_channels_in_order.eachWithIndex { channel, index -> if (index < required_channels_in_order.size() - 1) { - channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1])) + channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1])) } } if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + log.warn( + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + ) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index cbd8495b..b78273ca 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,13 +3,12 @@ // /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { - take: nextflow_cli_args @@ -22,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -33,12 +32,9 @@ workflow UTILS_NFCORE_PIPELINE { def checkConfigProvided() { def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " + log.warn( + "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " + ) valid_config = false } return valid_config @@ -49,12 +45,14 @@ def checkConfigProvided() { // def checkProfileProvided(nextflow_cli_args) { if (workflow.profile.endsWith(',')) { - error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + error( + "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } if (nextflow_cli_args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + log.warn( + "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } } @@ -70,13 +68,7 @@ def workflowCitation() { manifest_doi.each { doi_ref -> temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" } - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - temp_doi_ref + "\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } // @@ -102,7 +94,7 @@ def getWorkflowVersion() { // def processVersionsFromYAML(yaml_file) { def yaml = new org.yaml.snakeyaml.Yaml() - def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } return yaml.dumpAsMap(versions).trim() } @@ -112,8 +104,8 @@ def processVersionsFromYAML(yaml_file) { def workflowVersionToYAML() { return """ Workflow: - $workflow.manifest.name: ${getWorkflowVersion()} - Nextflow: $workflow.nextflow.version + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} """.stripIndent().trim() } @@ -121,11 +113,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions - .unique() - .map { version -> processVersionsFromYAML(version) } - .unique() - .mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) } // @@ -133,25 +121,31 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - summary_params.keySet().each { group -> - def group_params = summary_params.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

    \n" - summary_section += "
    \n" - group_params.keySet().sort().each { param -> - summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + summary_params + .keySet() + .each { group -> + def group_params = summary_params.get(group) + // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    ${group}

    \n" + summary_section += "
    \n" + group_params + .keySet() + .sort() + .each { param -> + summary_section += "
    ${param}
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" } - summary_section += "
    \n" } - } - def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" return yaml_file_text } @@ -199,54 +193,54 @@ def logColours(monochrome_logs=true) { colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" return colorcodes } @@ -261,14 +255,15 @@ def attachMultiqcReport(multiqc_report) { mqc_report = multiqc_report.getVal() if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") } mqc_report = mqc_report[0] } } - } catch (all) { + } + catch (Exception all) { if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") } } return mqc_report @@ -280,26 +275,35 @@ def attachMultiqcReport(multiqc_report) { def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" } def summary = [:] - summary_params.keySet().sort().each { group -> - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] misc_fields['Date Started'] = workflow.start misc_fields['Date Completed'] = workflow.complete misc_fields['Pipeline script file path'] = workflow.scriptFile misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build + if (workflow.repository) { + misc_fields['Pipeline repository Git URL'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['Pipeline repository Git Commit'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['Pipeline Git branch/tag'] = workflow.revision + } + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] @@ -337,7 +341,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Render the sendmail template def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_html = sendmail_template.toString() @@ -346,30 +350,32 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { +new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { + ['sendmail', '-t'].execute() << sendmail_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") + } + catch (Exception all) { // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") } } // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") output_tf.delete() } @@ -380,12 +386,14 @@ def completionSummary(monochrome_logs=true) { def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } @@ -394,21 +402,30 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - summary_params.keySet().sort().each { group -> - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) { + misc_fields['repository'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['commitid'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['revision'] = workflow.revision + } + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp def msg_fields = [:] msg_fields['version'] = getWorkflowVersion() @@ -433,13 +450,13 @@ def imNotification(summary_params, hook_url) { def json_message = json_template.toString() // POST - def post = new URL(hook_url).openConnection(); + def post = new URL(hook_url).openConnection() post.setRequestMethod("POST") post.setDoOutput(true) post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); + post.getOutputStream().write(json_message.getBytes("UTF-8")) + def postRC = post.getResponseCode() + if (!postRC.equals(200)) { + log.warn(post.getErrorStream().getText()) } } From cca4b1845c457b89fabc00d4efc22898b46d3ae5 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 11 Oct 2024 12:33:05 +0000 Subject: [PATCH 03/37] Template update for nf-core/tools version 3.0.2 --- .github/workflows/ci.yml | 60 +++++++++++++------ .../workflows/template_version_comment.yml | 21 ++++--- .gitignore | 1 + .nf-core.yml | 2 +- main.nf | 2 +- modules.json | 6 +- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 4 +- .../utils_nfcore_demultiplex_pipeline/main.nf | 4 +- .../nf-core/utils_nextflow_pipeline/main.nf | 30 +++++----- .../nf-core/utils_nfcore_pipeline/main.nf | 10 ++-- workflows/demultiplex.nf | 2 - 12 files changed, 86 insertions(+), 58 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ae05ff11..aa3e92fc 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -11,6 +11,8 @@ on: env: NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" @@ -18,7 +20,7 @@ concurrency: jobs: test: - name: Run pipeline with test data + name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" # Only run on push if this is the nf-core dev branch (merged PRs) if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/demultiplex') }}" runs-on: ubuntu-latest @@ -27,33 +29,57 @@ jobs: NXF_VER: - "24.04.2" - "latest-everything" + profile: + - "conda" + - "docker" + - "singularity" + test_name: + - "test" + isMaster: + - ${{ github.base_ref == 'master' }} + # Exclude conda and singularity on dev + exclude: + - isMaster: false + profile: "conda" + - isMaster: false + profile: "singularity" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Install Nextflow + - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" - - name: Disk space cleanup - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + - name: Set up Apptainer + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-apptainer@main - - name: Run pipeline with test data (docker) - # TODO nf-core: You can customise CI pipeline run tests as required - # For example: adding multiple test runs with different parameters - # Remember that you can parallelise this by using strategy.matrix + - name: Set up Singularity + if: matrix.profile == 'singularity' run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Set up Miniconda + if: matrix.profile == 'conda' + uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 + with: + miniconda-version: "latest" + auto-update-conda: true + conda-solver: libmamba + channels: conda-forge,bioconda - - name: Run pipeline with test data (singularity) - # TODO nf-core: You can customise CI pipeline run tests as required + - name: Set up Conda + if: matrix.profile == 'conda' run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results - if: "${{ github.base_ref == 'master' }}" + echo $(realpath $CONDA)/condabin >> $GITHUB_PATH + echo $(realpath python) >> $GITHUB_PATH + + - name: Clean up Disk space + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data (conda) - # TODO nf-core: You can customise CI pipeline run tests as required + - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results - if: "${{ github.base_ref == 'master' }}" + nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml index 9dea41f0..e8aafe44 100644 --- a/.github/workflows/template_version_comment.yml +++ b/.github/workflows/template_version_comment.yml @@ -10,9 +10,11 @@ jobs: steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + ref: ${{ github.event.pull_request.head.sha }} - name: Read template version from .nf-core.yml - uses: pietrobolcato/action-read-yaml@1.0.0 + uses: nichmor/minimal-read-yaml@v0.0.2 id: read_yml with: config: ${{ github.workspace }}/.nf-core.yml @@ -24,20 +26,21 @@ jobs: - name: Check nf-core outdated id: nf_core_outdated - run: pip list --outdated | grep nf-core + run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} - name: Post nf-core template version comment uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 if: | - ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core' + contains(env.OUTPUT, 'nf-core') with: repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} allow-repeats: false message: | - ## :warning: Newer version of the nf-core template is available. - - Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. - Please update your pipeline to the latest version. - - For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + > [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). # diff --git a/.gitignore b/.gitignore index 5124c9ac..a42ce016 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,4 @@ results/ testing/ testing* *.pyc +null/ diff --git a/.nf-core.yml b/.nf-core.yml index de3b862f..05ee5887 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -4,7 +4,7 @@ lint: files_unchanged: - .github/ISSUE_TEMPLATE/bug_report.yml - .github/workflows/linting.yml -nf_core_version: 3.0.1 +nf_core_version: 3.0.2 org_path: null repository_type: pipeline template: diff --git a/main.nf b/main.nf index c91a0de0..42a6f10c 100644 --- a/main.nf +++ b/main.nf @@ -76,7 +76,7 @@ workflow { params.outdir, params.input ) - + // // WORKFLOW: Run main workflow // diff --git a/modules.json b/modules.json index bcd1026f..eabc4c22 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c", + "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", "installed_by": ["modules"] } } @@ -21,12 +21,12 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", + "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", + "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 9724d2f3..cc0643e1 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -52,7 +52,7 @@ process MULTIQC { stub: """ mkdir multiqc_data - touch multiqc_plots + mkdir multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml diff --git a/nextflow.config b/nextflow.config index 2979d348..2ee0d50d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -254,10 +254,10 @@ validation { """ afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x + https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/${manifest.name}/blob/master/CITATIONS.md + https://github.com/${manifest.name}/blob/master/CITATIONS.md """ } summary { diff --git a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf index 8e2744f7..0dcdc78e 100644 --- a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf @@ -47,7 +47,6 @@ workflow PIPELINE_INITIALISATION { workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 ) - // // Validate parameters and generate parameter summary to stdout // @@ -56,7 +55,6 @@ workflow PIPELINE_INITIALISATION { validate_params, null ) - // // Check config provided to the pipeline @@ -64,6 +62,7 @@ workflow PIPELINE_INITIALISATION { UTILS_NFCORE_PIPELINE ( nextflow_cli_args ) + // // Custom validation for pipeline parameters // @@ -110,7 +109,6 @@ workflow PIPELINE_COMPLETION { email // string: email address email_on_fail // string: email address sent on pipeline failure plaintext_email // boolean: Send plain-text email instead of HTML - outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output hook_url // string: hook URL for notifications diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 2b0dc67a..0fcbf7b3 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { @@ -44,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -106,17 +106,19 @@ def checkCondaChannels() { def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - - required_channels_in_order.eachWithIndex { channel, index -> - if (index < required_channels_in_order.size() - 1) { - channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1])) - } - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { - log.warn( - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - ) + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index b78273ca..5cb7bafe 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { @@ -21,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -62,7 +62,7 @@ def checkProfileProvided(nextflow_cli_args) { def workflowCitation() { def temp_doi_ref = "" def manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs + // Handling multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list manifest_doi.each { doi_ref -> diff --git a/workflows/demultiplex.nf b/workflows/demultiplex.nf index e865b30a..478ac4a2 100644 --- a/workflows/demultiplex.nf +++ b/workflows/demultiplex.nf @@ -57,13 +57,11 @@ workflow DEMULTIPLEX { Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() - summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) ch_multiqc_files = ch_multiqc_files.mix( ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) From b313f82c9a171eaf97ce74bf14bc67eff2c59c19 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 14 Oct 2024 17:51:43 +0200 Subject: [PATCH 04/37] + verbose + debug in ci --- .github/workflows/ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7dce5ebb..6fc2c5d7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -103,6 +103,8 @@ jobs: - name: Run Tests (Shard ${{ matrix.shard }}/6) run: | nf-test test \ + --debug \ + --verbose \ --ci \ --shard ${{ matrix.shard }}/6 \ --changed-since HEAD^ \ From 9931615b15b7f92b945d3a889dcaca032c4731e4 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 14 Oct 2024 18:16:41 +0200 Subject: [PATCH 05/37] Apply suggestions from code review --- .github/workflows/download_pipeline.yml | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 713dc3e7..d3c9c2fb 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -69,7 +69,7 @@ jobs: --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" -l "ghcr.io" \ --container-cache-utilisation 'amend' \ --download-configuration 'yes' diff --git a/nextflow.config b/nextflow.config index 716d8b87..b3287d5d 100755 --- a/nextflow.config +++ b/nextflow.config @@ -285,7 +285,7 @@ validation { \033[0;35m ${manifest.name} ${manifest.version}\033[0m -\033[2m----------------------------------------------------\033[0m- """ - afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} + afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x From a0d482aa9e032146aa52ab3652ed2d761215103f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 14 Oct 2024 18:24:03 +0200 Subject: [PATCH 06/37] refactor tests --- nf-test.config | 4 + tests/pipeline/.nftignore | 1 + tests/pipeline/bases2fastq.nf.test | 31 +++---- tests/pipeline/bcl2fastq.nf.test | 30 +++--- tests/pipeline/bclconvert.nf.test | 30 +++--- tests/pipeline/bclconvert_mini.nf.test | 46 +++------- tests/pipeline/fqtk.nf.test | 69 +++----------- tests/pipeline/kraken.nf.test | 32 +++---- tests/pipeline/lib/UTILS.groovy | 11 --- tests/pipeline/mkfastq.nf.test | 44 +++------ tests/pipeline/sgdemux.nf.test | 74 +++------------ tests/pipeline/skip_tools.nf.test | 121 ++++++++++++++----------- tests/pipeline/test_pe.nf.test | 35 +++---- 13 files changed, 203 insertions(+), 325 deletions(-) create mode 100644 tests/pipeline/.nftignore delete mode 100644 tests/pipeline/lib/UTILS.groovy diff --git a/nf-test.config b/nf-test.config index a3837c71..d441a08a 100644 --- a/nf-test.config +++ b/nf-test.config @@ -13,5 +13,9 @@ config { // run all test with the defined docker profile from the main nextflow.config profile "docker,test" + + plugins { + load "nft-utils@0.0.3" + } } diff --git a/tests/pipeline/.nftignore b/tests/pipeline/.nftignore new file mode 100644 index 00000000..82580176 --- /dev/null +++ b/tests/pipeline/.nftignore @@ -0,0 +1 @@ +pipeline_info/*.{html,json,txt,yml} diff --git a/tests/pipeline/bases2fastq.nf.test b/tests/pipeline/bases2fastq.nf.test index 7a92b9d3..0a9288be 100644 --- a/tests/pipeline/bases2fastq.nf.test +++ b/tests/pipeline/bases2fastq.nf.test @@ -15,26 +15,23 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 8 }, + { assert workflow.success}, { assert snapshot( - // FIXME - // path("$outputDir/sim-data/DefaultSample_R1.fastq.gz.md5"), - // path("$outputDir/sim-data/DefaultSample_R2.fastq.gz.md5"), - path("$outputDir/sim-data/Metrics.csv"), - path("$outputDir/sim-data/UnassignedSequences.csv"), - path("$outputDir/sim-data/Samples/DefaultProject/DefaultSample/DefaultSample_R1.fastq.gz"), - path("$outputDir/sim-data/Samples/DefaultProject/DefaultSample/DefaultSample_R2.fastq.gz") - ).match("bases2fastq") }, - { assert new File("$outputDir/sim-data/20230404-Bases2Fastq-Sim_QC.html").exists() }, - { assert new File("$outputDir/sim-data/RunStats.json").exists() }, - { assert new File("$outputDir/sim-data/Samples/DefaultProject/DefaultSample/DefaultSample_stats.json").exists() }, - { assert new File("$outputDir/sim-data/RunManifest.json").exists() } + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } - } - } diff --git a/tests/pipeline/bcl2fastq.nf.test b/tests/pipeline/bcl2fastq.nf.test index 312ff522..59272e1d 100644 --- a/tests/pipeline/bcl2fastq.nf.test +++ b/tests/pipeline/bcl2fastq.nf.test @@ -15,25 +15,23 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 6 }, + { assert workflow.success}, { assert snapshot( - path("$outputDir/multiqc/multiqc_data/bcl2fastq_lane_counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/bcl2fastq_sample_counts.txt") - ).match("multiqc") }, - { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_summary.txt"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Stats/").list() - ).match("bcl2fastq") } + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } - } - } diff --git a/tests/pipeline/bclconvert.nf.test b/tests/pipeline/bclconvert.nf.test index ab3d93d0..08531bf5 100644 --- a/tests/pipeline/bclconvert.nf.test +++ b/tests/pipeline/bclconvert.nf.test @@ -15,25 +15,23 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 6 }, + { assert workflow.success}, { assert snapshot( - path("$outputDir/multiqc/multiqc_data/bclconvert_lane_counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/bclconvert_sample_counts_Counts_per_lane.txt") - ).match("multiqc") }, - { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_summary.txt"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - ).match("bclconvert") } + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } - } - } diff --git a/tests/pipeline/bclconvert_mini.nf.test b/tests/pipeline/bclconvert_mini.nf.test index 6f947349..6a9c04f0 100644 --- a/tests/pipeline/bclconvert_mini.nf.test +++ b/tests/pipeline/bclconvert_mini.nf.test @@ -15,41 +15,23 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 26 }, + { assert workflow.success}, { assert snapshot( - path("$outputDir/multiqc/multiqc_data/bclconvert_lane_counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/bclconvert_sample_counts_Counts_per_lane.txt") - ).match("multiqc") }, - { assert snapshot( - path("$outputDir/miniseq_truseq_smrna/HBRR1_S1_L001.fastp.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/HBRR1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/HBRR1_S1_L001_summary.txt"), - path("$outputDir/miniseq_truseq_smrna/HBRR2_S2_L001.fastp.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/HBRR2_S2_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/HBRR2_S2_L001_summary.txt"), - path("$outputDir/miniseq_truseq_smrna/HBRR3_S3_L001.fastp.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/HBRR3_S3_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/HBRR3_S3_L001_summary.txt"), - path("$outputDir/miniseq_truseq_smrna/UHRR1_S4_L001.fastp.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/UHRR1_S4_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/UHRR1_S4_L001_summary.txt"), - path("$outputDir/miniseq_truseq_smrna/UHRR2_S5_L001.fastp.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/UHRR2_S5_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/UHRR2_S5_L001_summary.txt"), - path("$outputDir/miniseq_truseq_smrna/UHRR3_S6_L001.fastp.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/UHRR3_S6_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/UHRR3_S6_L001_summary.txt"), - path("$outputDir/miniseq_truseq_smrna/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/Reports/").list(), - path("$outputDir/miniseq_truseq_smrna/InterOp/").list() - ).match("bclconvert") } + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } - } - } diff --git a/tests/pipeline/fqtk.nf.test b/tests/pipeline/fqtk.nf.test index 97dbd755..fb9c0883 100644 --- a/tests/pipeline/fqtk.nf.test +++ b/tests/pipeline/fqtk.nf.test @@ -14,61 +14,22 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 129 }, - { assert snapshot(path("$outputDir/test/demux-metrics.txt")).match("fqtk") }, - { assert new File("$outputDir/test/unmatched_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/unmatched_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s10_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s10_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s11_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s11_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s12_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s12_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s13_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s13_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s14_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s14_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s15_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s15_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s16_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s16_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s17_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s17_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s18_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s18_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s19_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s19_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s1_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s1_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s20_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s20_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s21_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s21_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s22_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s22_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s23_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s23_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s24_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s24_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s2_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s2_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s3_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s3_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s4_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s4_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s5_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s5_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s6_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s6_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s7_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s7_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s8_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s8_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s9_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s9_2.fastp.fastq.gz").exists() } + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } } diff --git a/tests/pipeline/kraken.nf.test b/tests/pipeline/kraken.nf.test index 0ee43998..aab87c59 100644 --- a/tests/pipeline/kraken.nf.test +++ b/tests/pipeline/kraken.nf.test @@ -21,27 +21,23 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 9 }, + { assert workflow.success}, { assert snapshot( - path("$outputDir/multiqc/multiqc_data/bcl2fastq_lane_counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/bcl2fastq_sample_counts.txt"), - path("$outputDir/multiqc/multiqc_data/kraken-top-n-plot.txt"), - ).match("multiqc") }, - { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.kraken2.report.txt"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_summary.txt"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Stats/").list(), - ).match("kraken") } + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } - } - } diff --git a/tests/pipeline/lib/UTILS.groovy b/tests/pipeline/lib/UTILS.groovy deleted file mode 100644 index deacb586..00000000 --- a/tests/pipeline/lib/UTILS.groovy +++ /dev/null @@ -1,11 +0,0 @@ -// Function to remove Nextflow version from software_versions.yml - -class UTILS { - public static String removeNextflowVersion(outputDir) { - def softwareVersions = path("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").yaml - if (softwareVersions.containsKey("Workflow")) { - softwareVersions.Workflow.remove("Nextflow") - } - return softwareVersions - } -} diff --git a/tests/pipeline/mkfastq.nf.test b/tests/pipeline/mkfastq.nf.test index 584656b7..12e5f27b 100644 --- a/tests/pipeline/mkfastq.nf.test +++ b/tests/pipeline/mkfastq.nf.test @@ -15,36 +15,22 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 10 }, - // How many directories were produced? - {assert path("${outputDir}").list().size() == 6}, - // How many files were produced? - {assert path("$outputDir/cellranger-tiny-bcl-simple/").list().size() == 2}, - {assert path("$outputDir/multiqc/").list().size() == 3}, - {assert path("$outputDir/pipeline_info/").list().size() == 5}, - // File assertions: Files that should be exactly the same with every pipeline execution. - {assert snapshot( - //Check output files - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_1.fastp.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_1.fastp.fastq.gz.md5"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_2.fastp.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_2.fastp.fastq.gz.md5"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz.md5"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_R1_001.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_R2_001.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_I1_001.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R1_001.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R2_001.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.html").exists(), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.html").exists(), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.json"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.json"), - path("${outputDir}/cellranger-tiny-bcl-simple/InterOp/IndexMetricsOut.bin") - ).match("file_assertions_mkfastq")} + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } } diff --git a/tests/pipeline/sgdemux.nf.test b/tests/pipeline/sgdemux.nf.test index 6539dec2..bc46c58a 100644 --- a/tests/pipeline/sgdemux.nf.test +++ b/tests/pipeline/sgdemux.nf.test @@ -15,69 +15,23 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 128 }, + { assert workflow.success}, { assert snapshot( - path("$outputDir/sim-data/metrics.tsv"), - path("$outputDir/sim-data/per_project_metrics.tsv"), - path("$outputDir/sim-data/per_sample_metrics.tsv"), - path("$outputDir/sim-data/sample_barcode_hop_metrics.tsv") - ).match("sgdemux") }, - { assert new File("$outputDir/sim-data/Undetermined_S25_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/Undetermined_S25_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s10_S10_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s10_S10_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s11_S11_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s11_S11_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s12_S12_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s12_S12_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s13_S13_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s13_S13_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s14_S14_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s14_S14_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s15_S15_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s15_S15_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s16_S16_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s16_S16_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s17_S17_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s17_S17_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s18_S18_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s18_S18_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s19_S19_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s19_S19_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s1_S1_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s1_S1_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s20_S20_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s20_S20_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s21_S21_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s21_S21_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s22_S22_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s22_S22_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s23_S23_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s23_S23_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s24_S24_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s24_S24_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s2_S2_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s2_S2_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s3_S3_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s3_S3_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s4_S4_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s4_S4_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s5_S5_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s5_S5_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s6_S6_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s6_S6_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s7_S7_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s7_S7_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s8_S8_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s8_S8_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s9_S9_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s9_S9_L001_2.fastp.fastq.gz").exists() } + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } - } - } diff --git a/tests/pipeline/skip_tools.nf.test b/tests/pipeline/skip_tools.nf.test index 4b9521ea..8a8bac90 100644 --- a/tests/pipeline/skip_tools.nf.test +++ b/tests/pipeline/skip_tools.nf.test @@ -19,20 +19,24 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_trimming") }, - { assert workflow.trace.succeeded().size() == 6 }, - { assert path("$outputDir/multiqc/multiqc_report.html").exists() }, + { assert workflow.success}, { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz.md5"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - ).match("skip_trimming") } + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } - } test("Skip Fastp") { @@ -47,20 +51,24 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_fastp") }, - { assert workflow.trace.succeeded().size() == 5 }, - { assert path("$outputDir/multiqc/multiqc_report.html").exists() }, + { assert workflow.success}, { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz.md5"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - ).match("skip_fastp") } + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } - } test("Skip Fastqc") { @@ -75,20 +83,24 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_fastqc") }, - { assert workflow.trace.succeeded().size() == 6 }, - { assert path("$outputDir/multiqc/multiqc_report.html").exists() }, + { assert workflow.success}, { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz.md5"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - ).match("skip_fastqc") } + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } - } test("Skip Fastp & Fastqc") { @@ -103,20 +115,24 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_fastp_fastqc") }, - { assert workflow.trace.succeeded().size() == 5 }, - { assert path("$outputDir/multiqc/multiqc_report.html").exists() }, + { assert workflow.success}, { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz.md5"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - ).match("skip_fastp_fastqc") } + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } - } test("Skip MultiQC") { @@ -131,20 +147,23 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_multiqc") }, - { assert workflow.trace.succeeded().size() == 5 }, - { assert !path("$outputDir/multiqc/multiqc_report.html").exists() }, + { assert workflow.success}, { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz.md5"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - ).match("skip_multiqc") } + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } - } - } diff --git a/tests/pipeline/test_pe.nf.test b/tests/pipeline/test_pe.nf.test index 94a61db6..58f8b4f6 100644 --- a/tests/pipeline/test_pe.nf.test +++ b/tests/pipeline/test_pe.nf.test @@ -15,30 +15,23 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 7 }, + { assert workflow.success}, { assert snapshot( - path("$outputDir/multiqc/multiqc_data/bcl2fastq_lane_counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/bcl2fastq_sample_counts.txt") - - ).match("multiqc") }, - { assert snapshot( - path("$outputDir/PE_Sample.lane1_no_adapters.csv"), - path("$outputDir/PE_Sample/L001/Sample1_S1_L001_1.fastp.fastq.gz"), - path("$outputDir/PE_Sample/L001/Sample1_S1_L001_2.fastp.fastq.gz"), - path("$outputDir/PE_Sample/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/PE_Sample/L001/Sample1_S1_L001_R2_001.fastq.gz"), - path("$outputDir/PE_Sample/L001/Sample1_S1_L001_1.fastp.fastq.gz_summary.txt"), - path("$outputDir/PE_Sample/L001/Sample1_S1_L001_2.fastp.fastq.gz_summary.txt"), - path("$outputDir/PE_Sample/L001/Reports/").list(), - path("$outputDir/PE_Sample/L001/Stats/").list() - ).match("bcl2fastq_pe") } + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } ) } - } - } From d5df903febfc41ecea25368236a2a0139d188acb Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 14 Oct 2024 18:29:47 +0200 Subject: [PATCH 07/37] fix doi text --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index b3287d5d..e3b0bf0e 100755 --- a/nextflow.config +++ b/nextflow.config @@ -285,7 +285,7 @@ validation { \033[0;35m ${manifest.name} ${manifest.version}\033[0m -\033[2m----------------------------------------------------\033[0m- """ - afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} + afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x From 6e8068f9ba05a1f9cb279214d4d8411b2445334d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 10:31:10 +0200 Subject: [PATCH 08/37] update pipeline tests and snapshots --- nextflow.config | 6 +- tests/pipeline/.nftignore | 6 + tests/pipeline/bases2fastq.nf.test | 2 +- tests/pipeline/bases2fastq.nf.test.snap | 260 +++++- tests/pipeline/bcl2fastq.nf.test | 2 +- tests/pipeline/bcl2fastq.nf.test.snap | 312 +++++-- tests/pipeline/bclconvert.nf.test | 2 +- tests/pipeline/bclconvert.nf.test.snap | 260 +++++- tests/pipeline/bclconvert_mini.nf.test | 2 +- tests/pipeline/bclconvert_mini.nf.test.snap | 310 +++++-- tests/pipeline/fqtk.nf.test | 2 +- tests/pipeline/fqtk.nf.test.snap | 257 ++++- tests/pipeline/kraken.nf.test | 2 +- tests/pipeline/kraken.nf.test.snap | 343 +++++-- tests/pipeline/mkfastq.nf.test | 2 +- tests/pipeline/mkfastq.nf.test.snap | 272 +++++- tests/pipeline/sgdemux.nf.test | 2 +- tests/pipeline/sgdemux.nf.test.snap | 260 +++++- tests/pipeline/skip_tools.nf.test | 10 +- tests/pipeline/skip_tools.nf.test.snap | 981 ++++++++++++++++++-- tests/pipeline/test_pe.nf.test | 2 +- tests/pipeline/test_pe.nf.test.snap | 316 +++++-- 22 files changed, 3099 insertions(+), 512 deletions(-) diff --git a/nextflow.config b/nextflow.config index e3b0bf0e..df00afee 100755 --- a/nextflow.config +++ b/nextflow.config @@ -72,6 +72,9 @@ params { // Load base.config by default for all pipelines includeConfig 'conf/base.config' +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' + profiles { debug { dumpHashes = true @@ -298,6 +301,3 @@ validation { afterText = validation.help.afterText } } - -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' diff --git a/tests/pipeline/.nftignore b/tests/pipeline/.nftignore index 82580176..1aa6f92c 100644 --- a/tests/pipeline/.nftignore +++ b/tests/pipeline/.nftignore @@ -1 +1,7 @@ +multiqc/multiqc_data/multiqc.log +multiqc/multiqc_data/multiqc_data.json +multiqc/multiqc_data/multiqc_software_versions.txt +multiqc/multiqc_data/multiqc_sources.txt +multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} +multiqc/multiqc_report.html pipeline_info/*.{html,json,txt,yml} diff --git a/tests/pipeline/bases2fastq.nf.test b/tests/pipeline/bases2fastq.nf.test index 0a9288be..71584e64 100644 --- a/tests/pipeline/bases2fastq.nf.test +++ b/tests/pipeline/bases2fastq.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/bases2fastq.nf.test.snap b/tests/pipeline/bases2fastq.nf.test.snap index fe10d197..88a60c02 100644 --- a/tests/pipeline/bases2fastq.nf.test.snap +++ b/tests/pipeline/bases2fastq.nf.test.snap @@ -1,25 +1,249 @@ { - "software_versions": { + "Bases2Fastq": { "content": [ - "{BASES2FASTQ={bases2fastq=1.8.0.1260801529, use subject to license available at elementbiosciences.com}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.2}}" + 6, + { + "BCLCONVERT": { + "bclconvert": "4.3.6" + }, + "FALCO": { + "falco": "1.2.1" + }, + "FASTP": { + "fastp": "0.23.4" + }, + "MD5SUM": { + "md5sum": 8.3 + }, + "Workflow": { + "nf-core/demultiplex": "v1.5.2" + } + }, + [ + "220422_M11111_0222_000000000-K9H97", + "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv", + "220422_M11111_0222_000000000-K9H97/InterOp", + "220422_M11111_0222_000000000-K9H97/InterOp/ControlMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/CorrectedIntMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/ErrorMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/ExtractionMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/IndexMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/QMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/TileMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/L001", + "220422_M11111_0222_000000000-K9H97/L001/Reports", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Adapter_Cycle_Metrics.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Adapter_Metrics.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Demultiplex_Stats.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Demultiplex_Tile_Stats.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/IndexMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Index_Hopping_Counts.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Quality_Metrics.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Quality_Tile_Metrics.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/RunInfo.xml", + "220422_M11111_0222_000000000-K9H97/L001/Reports/SampleSheet.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Top_Unknown_Barcodes.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/fastq_list.csv", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz.md5", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.html", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.json", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_fastqc_data.txt", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_report.html", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_summary.txt", + "220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz", + "fastq", + "fastq/Sample1_S1_L001.samplesheet.csv", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/bclconvert-lane-stats-table.txt", + "multiqc/multiqc_data/bclconvert-sample-stats-table.txt", + "multiqc/multiqc_data/bclconvert_lane_counts.txt", + "multiqc/multiqc_data/bclconvert_sample_counts_Counts_per_lane.txt", + "multiqc/multiqc_data/bclconvert_sample_counts_Index_mismatches.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp_filtered_reads_plot.txt", + "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc_bclconvert_bylane.txt", + "multiqc/multiqc_data/multiqc_bclconvert_bysample.txt", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_fastp.txt", + "multiqc/multiqc_data/multiqc_fastqc.txt", + "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/bclconvert-lane-stats-table.pdf", + "multiqc/multiqc_plots/pdf/bclconvert-sample-stats-table.pdf", + "multiqc/multiqc_plots/pdf/bclconvert_lane_counts-cnt.pdf", + "multiqc/multiqc_plots/pdf/bclconvert_lane_counts-pct.pdf", + "multiqc/multiqc_plots/pdf/bclconvert_sample_counts_Counts_per_lane-cnt.pdf", + "multiqc/multiqc_plots/pdf/bclconvert_sample_counts_Counts_per_lane-pct.pdf", + "multiqc/multiqc_plots/pdf/bclconvert_sample_counts_Index_mismatches-cnt.pdf", + "multiqc/multiqc_plots/pdf/bclconvert_sample_counts_Index_mismatches-pct.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_1_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_1_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_1_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_1_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp_filtered_reads_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastp_filtered_reads_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/multiqc_plots/pdf/general_stats_table.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/bclconvert-lane-stats-table.png", + "multiqc/multiqc_plots/png/bclconvert-sample-stats-table.png", + "multiqc/multiqc_plots/png/bclconvert_lane_counts-cnt.png", + "multiqc/multiqc_plots/png/bclconvert_lane_counts-pct.png", + "multiqc/multiqc_plots/png/bclconvert_sample_counts_Counts_per_lane-cnt.png", + "multiqc/multiqc_plots/png/bclconvert_sample_counts_Counts_per_lane-pct.png", + "multiqc/multiqc_plots/png/bclconvert_sample_counts_Index_mismatches-cnt.png", + "multiqc/multiqc_plots/png/bclconvert_sample_counts_Index_mismatches-pct.png", + "multiqc/multiqc_plots/png/fastp-seq-content-gc-plot_Read_1_After_filtering.png", + "multiqc/multiqc_plots/png/fastp-seq-content-gc-plot_Read_1_Before_filtering.png", + "multiqc/multiqc_plots/png/fastp-seq-content-n-plot_Read_1_After_filtering.png", + "multiqc/multiqc_plots/png/fastp-seq-content-n-plot_Read_1_Before_filtering.png", + "multiqc/multiqc_plots/png/fastp-seq-quality-plot_Read_1_After_filtering.png", + "multiqc/multiqc_plots/png/fastp-seq-quality-plot_Read_1_Before_filtering.png", + "multiqc/multiqc_plots/png/fastp_filtered_reads_plot-cnt.png", + "multiqc/multiqc_plots/png/fastp_filtered_reads_plot-pct.png", + "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", + "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/multiqc_plots/png/general_stats_table.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/bclconvert-lane-stats-table.svg", + "multiqc/multiqc_plots/svg/bclconvert-sample-stats-table.svg", + "multiqc/multiqc_plots/svg/bclconvert_lane_counts-cnt.svg", + "multiqc/multiqc_plots/svg/bclconvert_lane_counts-pct.svg", + "multiqc/multiqc_plots/svg/bclconvert_sample_counts_Counts_per_lane-cnt.svg", + "multiqc/multiqc_plots/svg/bclconvert_sample_counts_Counts_per_lane-pct.svg", + 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"multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", + "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4", + "samplesheet.csv:md5,b2f601061637b4d1227a4b755d594b6b" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-08T20:43:42.035230933" - }, - "multiqc": { - "content": [ - "bcl2fastq_lane_counts.txt:md5,9404ab530f43e442093337dd10c351c5", - "fastp_filtered_reads_plot.txt:md5,fa14a1941e109d4104c33db0e5fe20fc", - "bcl2fastq_sample_counts.txt:md5,93cb0cd1aee1b464f0e640e1c3d0c142" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.2" }, - "timestamp": "2024-08-08T20:43:42.016587995" + "timestamp": "2024-10-15T10:12:13.243489" } -} +} \ No newline at end of file diff --git a/tests/pipeline/bclconvert.nf.test b/tests/pipeline/bclconvert.nf.test index 08531bf5..9971db94 100644 --- a/tests/pipeline/bclconvert.nf.test +++ b/tests/pipeline/bclconvert.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/bclconvert.nf.test.snap b/tests/pipeline/bclconvert.nf.test.snap index 570ef214..f84c3737 100644 --- a/tests/pipeline/bclconvert.nf.test.snap +++ b/tests/pipeline/bclconvert.nf.test.snap @@ -1,11 +1,193 @@ { - "bclconvert": { + "BCL-CONVERT": { "content": [ - "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", - "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", - 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"bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", - "fastp_filtered_reads_plot.txt:md5,fa14a1941e109d4104c33db0e5fe20fc", - "bclconvert_sample_counts_Counts_per_lane.txt:md5,a7e57ab911ba2cf74ec7bd93b921036d" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nextflow": "24.09.2" }, - "timestamp": "2024-10-02T20:50:32.184940324" + "timestamp": "2024-10-15T10:13:39.908668" } -} +} \ No newline at end of file diff --git a/tests/pipeline/bclconvert_mini.nf.test b/tests/pipeline/bclconvert_mini.nf.test index 6a9c04f0..82fc94b3 100644 --- a/tests/pipeline/bclconvert_mini.nf.test +++ b/tests/pipeline/bclconvert_mini.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/bclconvert_mini.nf.test.snap b/tests/pipeline/bclconvert_mini.nf.test.snap index f837a605..c68bfea4 100644 --- a/tests/pipeline/bclconvert_mini.nf.test.snap +++ b/tests/pipeline/bclconvert_mini.nf.test.snap @@ -1,83 +1,249 @@ { - "bclconvert": { + "BCL-CONVERT-mini": { "content": [ - "HBRR1_S1_L001.fastp.fastq.gz:md5,451657490d4816dd5ff904e34ecc7fdf", - "HBRR1_S1_L001_R1_001.fastq.gz:md5,451657490d4816dd5ff904e34ecc7fdf", - "HBRR1_S1_L001_summary.txt:md5,53a5e6bac1e853f23d27d6966e52df81", - "HBRR2_S2_L001.fastp.fastq.gz:md5,3b9e4fc70ebc608b48d1f0027265e9b8", - "HBRR2_S2_L001_R1_001.fastq.gz:md5,3b9e4fc70ebc608b48d1f0027265e9b8", - "HBRR2_S2_L001_summary.txt:md5,f3e0bc27d30d0f6e10ad76be47017881", - 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}, - "timestamp": "2024-10-03T12:19:24.749587693" + "timestamp": "2024-10-15T10:15:05.102648" } -} +} \ No newline at end of file diff --git a/tests/pipeline/fqtk.nf.test b/tests/pipeline/fqtk.nf.test index fb9c0883..785de837 100644 --- a/tests/pipeline/fqtk.nf.test +++ b/tests/pipeline/fqtk.nf.test @@ -17,7 +17,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/fqtk.nf.test.snap b/tests/pipeline/fqtk.nf.test.snap index 005b38ff..ada01b9a 100644 --- 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- "nextflow": "24.04.4" - }, - "timestamp": "2024-10-02T20:52:55.269657852" + "timestamp": "2024-10-15T10:18:22.502979" } -} +} \ No newline at end of file diff --git a/tests/pipeline/mkfastq.nf.test b/tests/pipeline/mkfastq.nf.test index 12e5f27b..18efa05c 100644 --- a/tests/pipeline/mkfastq.nf.test +++ b/tests/pipeline/mkfastq.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/mkfastq.nf.test.snap b/tests/pipeline/mkfastq.nf.test.snap index 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"multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", + "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4", + "samplesheet.csv:md5,3bdee83c6b65bc3198c7742f4d19bfc9" + ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nextflow": "24.09.2" }, - "timestamp": "2024-08-02T19:58:24.75171605" - }, - "sgdemux": { - "content": [ - "metrics.tsv:md5,7627e4bd2a56ea551fd74b4a2b5cb4b2", - "per_project_metrics.tsv:md5,7393bc580c8ed8431107ad3dd00a7d2a", - "per_sample_metrics.tsv:md5,fb8ce024ad2508e7b22a4af65fe44358", - "sample_barcode_hop_metrics.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.4" - }, - "timestamp": "2023-10-17T08:01:14+0000" + "timestamp": "2024-10-15T10:21:44.426414" } -} +} \ No newline at end of file diff --git a/tests/pipeline/skip_tools.nf.test b/tests/pipeline/skip_tools.nf.test index 8a8bac90..9a388def 100644 --- a/tests/pipeline/skip_tools.nf.test +++ b/tests/pipeline/skip_tools.nf.test @@ -22,7 +22,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -54,7 +54,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -86,7 +86,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -118,7 +118,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -150,7 +150,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/skip_tools.nf.test.snap b/tests/pipeline/skip_tools.nf.test.snap index c30d5dac..b6e1e531 100644 --- a/tests/pipeline/skip_tools.nf.test.snap +++ b/tests/pipeline/skip_tools.nf.test.snap @@ -1,20 +1,155 @@ { - "software_versions_skip_trimming": { + "Skip Fastp & Fastqc": { "content": [ - "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.2}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-12T17:21:22.50969783" - }, - "skip_fastqc": { - "content": [ - "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", - "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", - "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", + 5, + { + "BCLCONVERT": { + "bclconvert": "4.3.6" + }, + "FALCO": { + "falco": "1.2.1" + }, + "MD5SUM": { + "md5sum": 8.3 + }, + "Workflow": { + "nf-core/demultiplex": "v1.5.2" + } + }, + [ + "220422_M11111_0222_000000000-K9H97", + "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv", + "220422_M11111_0222_000000000-K9H97/InterOp", + "220422_M11111_0222_000000000-K9H97/InterOp/ControlMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/CorrectedIntMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/ErrorMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/ExtractionMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/IndexMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/QMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/TileMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/L001", + "220422_M11111_0222_000000000-K9H97/L001/Reports", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Adapter_Cycle_Metrics.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Adapter_Metrics.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Demultiplex_Stats.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Demultiplex_Tile_Stats.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/IndexMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Index_Hopping_Counts.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Quality_Metrics.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Quality_Tile_Metrics.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/RunInfo.xml", + "220422_M11111_0222_000000000-K9H97/L001/Reports/SampleSheet.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Top_Unknown_Barcodes.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/fastq_list.csv", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz.md5", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_fastqc_data.txt", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_report.html", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_summary.txt", + "220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz", + "fastq", + "fastq/Sample1_S1_L001.samplesheet.csv", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/bclconvert-lane-stats-table.txt", + "multiqc/multiqc_data/bclconvert-sample-stats-table.txt", + "multiqc/multiqc_data/bclconvert_lane_counts.txt", + "multiqc/multiqc_data/bclconvert_sample_counts_Counts_per_lane.txt", + "multiqc/multiqc_data/bclconvert_sample_counts_Index_mismatches.txt", + "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc_bclconvert_bylane.txt", + "multiqc/multiqc_data/multiqc_bclconvert_bysample.txt", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_fastqc.txt", + "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/bclconvert-lane-stats-table.pdf", + "multiqc/multiqc_plots/pdf/bclconvert-sample-stats-table.pdf", + "multiqc/multiqc_plots/pdf/bclconvert_lane_counts-cnt.pdf", + "multiqc/multiqc_plots/pdf/bclconvert_lane_counts-pct.pdf", + "multiqc/multiqc_plots/pdf/bclconvert_sample_counts_Counts_per_lane-cnt.pdf", + "multiqc/multiqc_plots/pdf/bclconvert_sample_counts_Counts_per_lane-pct.pdf", + 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"220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c", + "ControlMetricsOut.bin:md5,6d77b38d0793a6e1ce1e85706e488953", + "CorrectedIntMetricsOut.bin:md5,2bbf84d3be72734addaa2fe794711434", + "ErrorMetricsOut.bin:md5,38c88def138e9bb832539911affdb286", + "ExtractionMetricsOut.bin:md5,7497c3178837eea8f09350b5cd252e99", + "IndexMetricsOut.bin:md5,d41d8cd98f00b204e9800998ecf8427e", + "QMetricsOut.bin:md5,7e9f198d53ebdfbb699a5f94cf1ed51c", + "TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c", "Adapter_Cycle_Metrics.csv:md5,5a0c88793b4a0885fe3dda16609b576e", "Adapter_Metrics.csv:md5,989240b8840b2169ac1061f952c90f6c", "Demultiplex_Stats.csv:md5,93949a8cd96f907d83e0808c1ec2a04b", @@ -170,13 +941,51 @@ "RunInfo.xml:md5,03038959f4dd181c86bc97ae71fe270a", "SampleSheet.csv:md5,ee5db2e12754e069998b0a96e535238c", "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc", - "fastq_list.csv:md5,ae1470cd741e33b87a4ad26f849a50f9" + "fastq_list.csv:md5,ae1470cd741e33b87a4ad26f849a50f9", + "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", + "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", + "Sample1_S1_L001.fastp.html:md5,891a4790630e04c0887b8e6ffe06ea5d", + "Sample1_S1_L001.fastp.json:md5,d9d2d702f3c64412a04cd0768863b1ab", + "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", + "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", + "Sample1_S1_L001_report.html:md5,fbca1db2e238255ba2237f963aa38000", + "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", + "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", + "Sample1_S1_L001.samplesheet.csv:md5,5aa2de9a3b6807a3e077081b45c4187a", + "bclconvert-lane-stats-table.txt:md5,8bff7b728d3ad67405d4742d0aa2088e", + "bclconvert-sample-stats-table.txt:md5,a6edf6b192981bd296c1eba968e4333c", + "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", + "bclconvert_sample_counts_Counts_per_lane.txt:md5,a7e57ab911ba2cf74ec7bd93b921036d", + "bclconvert_sample_counts_Index_mismatches.txt:md5,06c29164e83815c79a2b1541a4a6294e", + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,8105d4ce1d752e1f8a26e4291e8d9c6c", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,0ac68e41c4de8ca35a1cd6ee7c6cb3f3", + "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,1ec69a9fd0d46a39dfb59e377733e98b", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,1ec69a9fd0d46a39dfb59e377733e98b", + "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,1701b40c23dca068210f5410788e3be1", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,35de9aebdc467b1bbc9fd1f40d3aece4", + "fastp_filtered_reads_plot.txt:md5,fa14a1941e109d4104c33db0e5fe20fc", + "fastqc-status-check-heatmap.txt:md5,ba346b48736a57f50aa1ef5ce468f5df", + "fastqc_per_base_n_content_plot.txt:md5,d7db99124db8f53d82c51c779ce77463", + "fastqc_per_base_sequence_quality_plot.txt:md5,31c51bbd7d4dbb32107efa95c8a58ee5", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,842eaa1c62a8e6676b4b07226bda998b", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b231390d458d0bfdf4fa1360a776e03c", + "fastqc_per_sequence_quality_scores_plot.txt:md5,edbe64e0545cb866af73a649349d2a42", + "fastqc_sequence_counts_plot.txt:md5,662c69090978601ca7d39504b1ac736b", + "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", + "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", + "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", + "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", + "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", + "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4", + "samplesheet.csv:md5,5aa2de9a3b6807a3e077081b45c4187a" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.2" }, - "timestamp": "2024-08-12T17:21:22.530325808" + "timestamp": "2024-10-15T10:26:03.680342" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_pe.nf.test b/tests/pipeline/test_pe.nf.test index 58f8b4f6..1663c0d6 100644 --- a/tests/pipeline/test_pe.nf.test +++ b/tests/pipeline/test_pe.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/test_pe.nf.test.snap b/tests/pipeline/test_pe.nf.test.snap index d93f5470..1faeb21f 100644 --- a/tests/pipeline/test_pe.nf.test.snap +++ b/tests/pipeline/test_pe.nf.test.snap @@ -1,89 +1,249 @@ { - "bcl2fastq_pe": { + "Bcl2Fastq_pe": { "content": [ - "PE_Sample.lane1_no_adapters.csv:md5,c31cca10b3a1aed8ec68daf779217d91", - "Sample1_S1_L001_1.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", - "Sample1_S1_L001_2.fastp.fastq.gz:md5,adbc8e47c8e7e902777a01ea3d73b306", - "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", - "Sample1_S1_L001_R2_001.fastq.gz:md5,146eefcab1eaaef17ffb72672c021368", - "Sample1_S1_L001_1.fastp.fastq.gz_summary.txt:md5,917b542afe3e3f178b994317c955ce02", - "Sample1_S1_L001_2.fastp.fastq.gz_summary.txt:md5,441197ccd90d2b018db631a66d6fbbb3", + 6, + { + "BCLCONVERT": { + "bclconvert": 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"Demultiplex_Tile_Stats.csv:md5,83120160b0f22a1303fa1db31c19f6e9", + "IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf", + "Index_Hopping_Counts.csv:md5,1059369e375fd8f8423c0f6c934be978", + "Quality_Metrics.csv:md5,6614accb1bb414fe312b17b81f5521f7", + "Quality_Tile_Metrics.csv:md5,cdc89fd2962bdd4a24f71e186112118a", + "RunInfo.xml:md5,03038959f4dd181c86bc97ae71fe270a", + "SampleSheet.csv:md5,ee5db2e12754e069998b0a96e535238c", + "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc", + "fastq_list.csv:md5,ae1470cd741e33b87a4ad26f849a50f9", + "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", + "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", + "Sample1_S1_L001.fastp.html:md5,e8775bff2ee6c4ac246425febc88fc71", + "Sample1_S1_L001.fastp.json:md5,d9d2d702f3c64412a04cd0768863b1ab", + "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", + "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", + "Sample1_S1_L001_report.html:md5,194a1a45b6cd90461a1f0d7beee627bb", + "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", + "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", + "Sample1_S1_L001.samplesheet.csv:md5,7ded6e3f2420a20eb577f930914fd137", + "bclconvert-lane-stats-table.txt:md5,8bff7b728d3ad67405d4742d0aa2088e", + "bclconvert-sample-stats-table.txt:md5,a6edf6b192981bd296c1eba968e4333c", + "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", + "bclconvert_sample_counts_Counts_per_lane.txt:md5,a7e57ab911ba2cf74ec7bd93b921036d", + "bclconvert_sample_counts_Index_mismatches.txt:md5,06c29164e83815c79a2b1541a4a6294e", + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,8105d4ce1d752e1f8a26e4291e8d9c6c", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,0ac68e41c4de8ca35a1cd6ee7c6cb3f3", + "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,1ec69a9fd0d46a39dfb59e377733e98b", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,1ec69a9fd0d46a39dfb59e377733e98b", + "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,1701b40c23dca068210f5410788e3be1", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,35de9aebdc467b1bbc9fd1f40d3aece4", + "fastp_filtered_reads_plot.txt:md5,fa14a1941e109d4104c33db0e5fe20fc", + "fastqc-status-check-heatmap.txt:md5,ba346b48736a57f50aa1ef5ce468f5df", + "fastqc_per_base_n_content_plot.txt:md5,d7db99124db8f53d82c51c779ce77463", + "fastqc_per_base_sequence_quality_plot.txt:md5,31c51bbd7d4dbb32107efa95c8a58ee5", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,842eaa1c62a8e6676b4b07226bda998b", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b231390d458d0bfdf4fa1360a776e03c", + "fastqc_per_sequence_quality_scores_plot.txt:md5,edbe64e0545cb866af73a649349d2a42", + "fastqc_sequence_counts_plot.txt:md5,662c69090978601ca7d39504b1ac736b", + "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", + "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", + "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", + "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", + "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", + "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4", + "samplesheet.csv:md5,7ded6e3f2420a20eb577f930914fd137" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "23.10.1" + "nextflow": "24.09.2" }, - "timestamp": "2024-08-07T15:19:05.728175" - }, - "software_versions": { - "content": [ - "{BCL2FASTQ={bcl2fastq=2.20.0.422}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.2}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-31T13:03:01.047096473" - }, - "multiqc": { - "content": [ - "bcl2fastq_lane_counts.txt:md5,d6054e1ec3c2e8d33c3fdee5b250dfbc", - "fastp_filtered_reads_plot.txt:md5,136a1d755ba6e790227f80cfcb4c1d62", - "bcl2fastq_sample_counts.txt:md5,93cb0cd1aee1b464f0e640e1c3d0c142" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-01T16:33:58.242361926" + "timestamp": "2024-10-15T10:30:20.199021" } -} +} \ No newline at end of file From 856d73b29090f63e648aa832b1cdb50f9d24f101 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 15 Oct 2024 10:45:03 +0200 Subject: [PATCH 09/37] Update conf/base.config --- conf/base.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/base.config b/conf/base.config index 93a88889..6f1752f4 100755 --- a/conf/base.config +++ b/conf/base.config @@ -10,7 +10,6 @@ process { - // TODO nf-core: Check the defaults for all processes cpus = { 1 * task.attempt } memory = { 6.GB * task.attempt } time = { 4.h * task.attempt } From 053fc10010f7183cb9777c57fc17db0c0f7b09d3 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 15 Oct 2024 10:48:16 +0200 Subject: [PATCH 10/37] Update .github/workflows/ci.yml --- .github/workflows/ci.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6fc2c5d7..6fef5f23 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -35,7 +35,6 @@ jobs: - "24.04.2" - "latest-everything" profile: - - "conda" - "docker" - "singularity" isMaster: From e47687f1da41b8c18e77e61537e7dcf3a0454d42 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 11:01:36 +0200 Subject: [PATCH 11/37] update .nftignore --- tests/pipeline/.nftignore | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/pipeline/.nftignore b/tests/pipeline/.nftignore index 1aa6f92c..923950bc 100644 --- a/tests/pipeline/.nftignore +++ b/tests/pipeline/.nftignore @@ -1,3 +1,6 @@ +**/*.fastp.html +**/*_report.html +fastq/*.samplesheet.csv multiqc/multiqc_data/multiqc.log multiqc/multiqc_data/multiqc_data.json multiqc/multiqc_data/multiqc_software_versions.txt @@ -5,3 +8,4 @@ multiqc/multiqc_data/multiqc_sources.txt multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html pipeline_info/*.{html,json,txt,yml} +samplesheet/samplesheet.csv From 008b4ac0bdf8f7a95b35b9d0db951ae6b85fcd36 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 11:28:46 +0200 Subject: [PATCH 12/37] update snapshots --- tests/pipeline/bases2fastq.nf.test.snap | 8 +- tests/pipeline/bcl2fastq.nf.test.snap | 8 +- tests/pipeline/bclconvert.nf.test.snap | 8 +- tests/pipeline/bclconvert_mini.nf.test.snap | 8 +- tests/pipeline/fqtk.nf.test.snap | 8 +- tests/pipeline/kraken.nf.test.snap | 8 +- tests/pipeline/mkfastq.nf.test.snap | 8 +- tests/pipeline/sgdemux.nf.test.snap | 8 +- tests/pipeline/skip_tools.nf.test.snap | 324 +++++++++----------- tests/pipeline/test_pe.nf.test.snap | 8 +- 10 files changed, 171 insertions(+), 225 deletions(-) diff --git a/tests/pipeline/bases2fastq.nf.test.snap b/tests/pipeline/bases2fastq.nf.test.snap index 88a60c02..c63ef982 100644 --- a/tests/pipeline/bases2fastq.nf.test.snap +++ b/tests/pipeline/bases2fastq.nf.test.snap @@ -202,14 +202,11 @@ "fastq_list.csv:md5,ae1470cd741e33b87a4ad26f849a50f9", "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", - "Sample1_S1_L001.fastp.html:md5,c048d31e8b5ae3750a2472e9b1d15dd2", "Sample1_S1_L001.fastp.json:md5,d9d2d702f3c64412a04cd0768863b1ab", "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", - "Sample1_S1_L001_report.html:md5,e2252c40edd00317cea86a9689869b30", "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "Sample1_S1_L001.samplesheet.csv:md5,bd224699e8306dcc3df78c6eea26f100", "bclconvert-lane-stats-table.txt:md5,8bff7b728d3ad67405d4742d0aa2088e", "bclconvert-sample-stats-table.txt:md5,a6edf6b192981bd296c1eba968e4333c", "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", @@ -236,14 +233,13 @@ "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", - "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4", - "samplesheet.csv:md5,bd224699e8306dcc3df78c6eea26f100" + "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T10:10:48.63615" + "timestamp": "2024-10-15T11:03:18.330528" } } \ No newline at end of file diff --git a/tests/pipeline/bcl2fastq.nf.test.snap b/tests/pipeline/bcl2fastq.nf.test.snap index ea594ae9..0248ec7a 100644 --- a/tests/pipeline/bcl2fastq.nf.test.snap +++ b/tests/pipeline/bcl2fastq.nf.test.snap @@ -202,14 +202,11 @@ "fastq_list.csv:md5,ae1470cd741e33b87a4ad26f849a50f9", "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", - "Sample1_S1_L001.fastp.html:md5,08e5cb8ab1eb890ede048317cdc85c78", "Sample1_S1_L001.fastp.json:md5,d9d2d702f3c64412a04cd0768863b1ab", "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", - "Sample1_S1_L001_report.html:md5,2d9ec6c927985375b76190e4b88e0889", "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "Sample1_S1_L001.samplesheet.csv:md5,b2f601061637b4d1227a4b755d594b6b", "bclconvert-lane-stats-table.txt:md5,8bff7b728d3ad67405d4742d0aa2088e", "bclconvert-sample-stats-table.txt:md5,a6edf6b192981bd296c1eba968e4333c", "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", @@ -236,14 +233,13 @@ "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", - "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4", - "samplesheet.csv:md5,b2f601061637b4d1227a4b755d594b6b" + "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T10:12:13.243489" + "timestamp": "2024-10-15T11:04:51.596382" } } \ No newline at end of file diff --git a/tests/pipeline/bclconvert.nf.test.snap b/tests/pipeline/bclconvert.nf.test.snap index f84c3737..c274e21e 100644 --- a/tests/pipeline/bclconvert.nf.test.snap +++ b/tests/pipeline/bclconvert.nf.test.snap @@ -202,14 +202,11 @@ "fastq_list.csv:md5,ae1470cd741e33b87a4ad26f849a50f9", "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", - "Sample1_S1_L001.fastp.html:md5,71b5d22a967fe1e5cbd9a777d2bcdc6d", "Sample1_S1_L001.fastp.json:md5,d9d2d702f3c64412a04cd0768863b1ab", "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", - "Sample1_S1_L001_report.html:md5,47092539f76962837c61e0aa9cf81626", "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "Sample1_S1_L001.samplesheet.csv:md5,407d6833fc2f7b21ff732912926eef63", "bclconvert-lane-stats-table.txt:md5,8bff7b728d3ad67405d4742d0aa2088e", "bclconvert-sample-stats-table.txt:md5,a6edf6b192981bd296c1eba968e4333c", "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", @@ -236,14 +233,13 @@ "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", - "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4", - "samplesheet.csv:md5,407d6833fc2f7b21ff732912926eef63" + "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T10:13:39.908668" + "timestamp": "2024-10-15T11:06:25.196456" } } \ No newline at end of file diff --git a/tests/pipeline/bclconvert_mini.nf.test.snap b/tests/pipeline/bclconvert_mini.nf.test.snap index c68bfea4..592885cf 100644 --- a/tests/pipeline/bclconvert_mini.nf.test.snap +++ b/tests/pipeline/bclconvert_mini.nf.test.snap @@ -202,14 +202,11 @@ "fastq_list.csv:md5,ae1470cd741e33b87a4ad26f849a50f9", "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", - "Sample1_S1_L001.fastp.html:md5,18f55c529a3815d35a7e65f9eaf5ac09", "Sample1_S1_L001.fastp.json:md5,d9d2d702f3c64412a04cd0768863b1ab", "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", - "Sample1_S1_L001_report.html:md5,4bf4274eec173b962c6d242049ac270f", "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "Sample1_S1_L001.samplesheet.csv:md5,13adb61df2adee8226c7af4ce3b0f6a5", "bclconvert-lane-stats-table.txt:md5,8bff7b728d3ad67405d4742d0aa2088e", "bclconvert-sample-stats-table.txt:md5,a6edf6b192981bd296c1eba968e4333c", "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", @@ -236,14 +233,13 @@ "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", - "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4", - "samplesheet.csv:md5,13adb61df2adee8226c7af4ce3b0f6a5" + "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T10:15:05.102648" + "timestamp": "2024-10-15T11:07:59.407222" } } \ No newline at end of file diff --git a/tests/pipeline/fqtk.nf.test.snap b/tests/pipeline/fqtk.nf.test.snap index ada01b9a..b93a87e7 100644 --- a/tests/pipeline/fqtk.nf.test.snap +++ b/tests/pipeline/fqtk.nf.test.snap @@ -202,14 +202,11 @@ "fastq_list.csv:md5,ae1470cd741e33b87a4ad26f849a50f9", "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", - "Sample1_S1_L001.fastp.html:md5,f8c2a42da224b7af3b8b5460491ca140", "Sample1_S1_L001.fastp.json:md5,d9d2d702f3c64412a04cd0768863b1ab", "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", - "Sample1_S1_L001_report.html:md5,7a7719506bfc2e7f4481cd69bfdf6007", "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "Sample1_S1_L001.samplesheet.csv:md5,f479e93c488d73163c61ce4e40000d97", "bclconvert-lane-stats-table.txt:md5,8bff7b728d3ad67405d4742d0aa2088e", "bclconvert-sample-stats-table.txt:md5,a6edf6b192981bd296c1eba968e4333c", "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", @@ -236,14 +233,13 @@ "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", - "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4", - "samplesheet.csv:md5,f479e93c488d73163c61ce4e40000d97" + "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T10:16:38.79096" + "timestamp": "2024-10-15T11:09:29.744077" } } \ No newline at end of file diff --git a/tests/pipeline/kraken.nf.test.snap b/tests/pipeline/kraken.nf.test.snap index 28795bbc..543683ef 100644 --- a/tests/pipeline/kraken.nf.test.snap +++ b/tests/pipeline/kraken.nf.test.snap @@ -229,13 +229,11 @@ "tree.html:md5,a1b9bf592973ca829ec69ddf888b7e34", "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", - "Sample1_S1_L001.fastp.html:md5,c45131c81bf72c16afdbb3c63a6cae3d", "Sample1_S1_L001.fastp.json:md5,d9d2d702f3c64412a04cd0768863b1ab", "Sample1_S1_L001.kraken2.report.txt:md5,726f60beda853ebb9134f6a712c4196b", "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", "Sample1_S1_L001_Sample1_S1_L001.fastp.fastq.gz:md5,53bf34dad1f8269eeed36e661ef036fb", "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", - "Sample1_S1_L001_report.html:md5,92d51c9726f30cfd2d0cf7c6d245fc61", "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", "AdapterTrimming.txt:md5,48ed2b914b1246c0b5d8667525550946", "ConversionStats.xml:md5,a2eaeb8dab2e605db56af05c53855f55", @@ -243,7 +241,6 @@ "DemuxSummaryF1L1.txt:md5,f9782d533f8ac08e2f107f681068c605", "FastqSummaryF1L1.txt:md5,0c6f2d87ee183b84d1051cde9a5643d1", "Stats.json:md5,199fdf6292e0250385110bebca28b2dc", - "Sample1_S1_L001.samplesheet.csv:md5,70049a6ff8851343acd078e00ff54781", "bcl2fastq-lane-stats-table.txt:md5,d0e821a9c0ccf7da808c5dd05e99ddc2", "bcl2fastq_lane_counts.txt:md5,9404ab530f43e442093337dd10c351c5", "bcl2fastq_sample_counts.txt:md5,93cb0cd1aee1b464f0e640e1c3d0c142", @@ -271,14 +268,13 @@ "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", "multiqc_general_stats.txt:md5,2b86df713f6998ec0468bc4c9a6ec7a3", - "multiqc_kraken.txt:md5,a90fd69786a0df1e43b948e423545654", - "samplesheet.csv:md5,70049a6ff8851343acd078e00ff54781" + "multiqc_kraken.txt:md5,a90fd69786a0df1e43b948e423545654" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T10:18:22.502979" + "timestamp": "2024-10-15T11:11:03.560171" } } \ No newline at end of file diff --git a/tests/pipeline/mkfastq.nf.test.snap b/tests/pipeline/mkfastq.nf.test.snap index 8023096c..f25bc158 100644 --- a/tests/pipeline/mkfastq.nf.test.snap +++ b/tests/pipeline/mkfastq.nf.test.snap @@ -202,14 +202,11 @@ "fastq_list.csv:md5,ae1470cd741e33b87a4ad26f849a50f9", "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", - "Sample1_S1_L001.fastp.html:md5,d3a3d8c6a2603ccf0753b5d5997c4c3f", "Sample1_S1_L001.fastp.json:md5,d9d2d702f3c64412a04cd0768863b1ab", "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", - "Sample1_S1_L001_report.html:md5,1442f9d2a29fde9f858fe798996c32d2", "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "Sample1_S1_L001.samplesheet.csv:md5,8960beef02ac0cd2e839c5f492a4f168", "bclconvert-lane-stats-table.txt:md5,8bff7b728d3ad67405d4742d0aa2088e", "bclconvert-sample-stats-table.txt:md5,a6edf6b192981bd296c1eba968e4333c", "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", @@ -236,14 +233,13 @@ "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", - "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4", - "samplesheet.csv:md5,8960beef02ac0cd2e839c5f492a4f168" + "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T10:20:06.612569" + "timestamp": "2024-10-15T11:12:31.672445" } } \ No newline at end of file diff --git a/tests/pipeline/sgdemux.nf.test.snap b/tests/pipeline/sgdemux.nf.test.snap index 77941b60..e84b0494 100644 --- a/tests/pipeline/sgdemux.nf.test.snap +++ b/tests/pipeline/sgdemux.nf.test.snap @@ -202,14 +202,11 @@ "fastq_list.csv:md5,ae1470cd741e33b87a4ad26f849a50f9", "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", - "Sample1_S1_L001.fastp.html:md5,c05e07d40a86c4c5ca0d850dc01813ad", "Sample1_S1_L001.fastp.json:md5,d9d2d702f3c64412a04cd0768863b1ab", "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", - "Sample1_S1_L001_report.html:md5,5dfbb79d210dbff4d9e39f23c340a236", "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "Sample1_S1_L001.samplesheet.csv:md5,3bdee83c6b65bc3198c7742f4d19bfc9", "bclconvert-lane-stats-table.txt:md5,8bff7b728d3ad67405d4742d0aa2088e", "bclconvert-sample-stats-table.txt:md5,a6edf6b192981bd296c1eba968e4333c", "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", @@ -236,14 +233,13 @@ "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", - "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4", - "samplesheet.csv:md5,3bdee83c6b65bc3198c7742f4d19bfc9" + "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T10:21:44.426414" + "timestamp": "2024-10-15T11:14:01.925212" } } \ No newline at end of file diff --git a/tests/pipeline/skip_tools.nf.test.snap b/tests/pipeline/skip_tools.nf.test.snap index b6e1e531..72cc2578 100644 --- a/tests/pipeline/skip_tools.nf.test.snap +++ b/tests/pipeline/skip_tools.nf.test.snap @@ -1,5 +1,5 @@ { - "Skip Fastp & Fastqc": { + "Skip Fastp": { "content": [ 5, { @@ -165,10 +165,8 @@ "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", "Sample1_S1_L001_R1_001.fastq.gz.md5:md5,10295d4e5ca66dae7788bbf24886cded", "Sample1_S1_L001_fastqc_data.txt:md5,dc27b3ffca4e60d28ab31bba42bdb551", - "Sample1_S1_L001_report.html:md5,ad04e5faf45c30d651892e72f32a1de1", "Sample1_S1_L001_summary.txt:md5,37bccdcaa1e1fe1022adebf2abad9121", "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "Sample1_S1_L001.samplesheet.csv:md5,73b3501bfad8ab1f27b1ddb37dac50b3", "bclconvert-lane-stats-table.txt:md5,8bff7b728d3ad67405d4742d0aa2088e", "bclconvert-sample-stats-table.txt:md5,a6edf6b192981bd296c1eba968e4333c", "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", @@ -187,19 +185,18 @@ "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "multiqc_fastqc.txt:md5,a894d852b250ee902d805b358c173b88", - "multiqc_general_stats.txt:md5,9e6cd051b09056263f269029b21a643b", - "samplesheet.csv:md5,73b3501bfad8ab1f27b1ddb37dac50b3" + "multiqc_general_stats.txt:md5,9e6cd051b09056263f269029b21a643b" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T10:27:04.91507" + "timestamp": "2024-10-15T11:16:29.215413" }, - "Skip Fastp": { + "Skip Trimming": { "content": [ - 5, + 6, { "BCLCONVERT": { "bclconvert": "4.3.6" @@ -207,6 +204,9 @@ "FALCO": { "falco": "1.2.1" }, + "FASTP": { + "fastp": "0.23.4" + }, "MD5SUM": { "md5sum": 8.3 }, @@ -239,6 +239,8 @@ "220422_M11111_0222_000000000-K9H97/L001/Reports/SampleSheet.csv", "220422_M11111_0222_000000000-K9H97/L001/Reports/Top_Unknown_Barcodes.csv", "220422_M11111_0222_000000000-K9H97/L001/Reports/fastq_list.csv", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.html", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.json", "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz", "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz.md5", "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_fastqc_data.txt", @@ -254,6 +256,13 @@ "multiqc/multiqc_data/bclconvert_lane_counts.txt", "multiqc/multiqc_data/bclconvert_sample_counts_Counts_per_lane.txt", "multiqc/multiqc_data/bclconvert_sample_counts_Index_mismatches.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp_filtered_reads_plot.txt", "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", @@ -268,6 +277,7 @@ "multiqc/multiqc_data/multiqc_bclconvert_bysample.txt", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_fastp.txt", "multiqc/multiqc_data/multiqc_fastqc.txt", "multiqc/multiqc_data/multiqc_general_stats.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", @@ -282,6 +292,14 @@ "multiqc/multiqc_plots/pdf/bclconvert_sample_counts_Counts_per_lane-pct.pdf", "multiqc/multiqc_plots/pdf/bclconvert_sample_counts_Index_mismatches-cnt.pdf", "multiqc/multiqc_plots/pdf/bclconvert_sample_counts_Index_mismatches-pct.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_1_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_1_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_1_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_1_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp_filtered_reads_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastp_filtered_reads_plot-pct.pdf", "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", @@ -302,6 +320,14 @@ "multiqc/multiqc_plots/png/bclconvert_sample_counts_Counts_per_lane-pct.png", "multiqc/multiqc_plots/png/bclconvert_sample_counts_Index_mismatches-cnt.png", "multiqc/multiqc_plots/png/bclconvert_sample_counts_Index_mismatches-pct.png", + "multiqc/multiqc_plots/png/fastp-seq-content-gc-plot_Read_1_After_filtering.png", + "multiqc/multiqc_plots/png/fastp-seq-content-gc-plot_Read_1_Before_filtering.png", + "multiqc/multiqc_plots/png/fastp-seq-content-n-plot_Read_1_After_filtering.png", + "multiqc/multiqc_plots/png/fastp-seq-content-n-plot_Read_1_Before_filtering.png", + "multiqc/multiqc_plots/png/fastp-seq-quality-plot_Read_1_After_filtering.png", + "multiqc/multiqc_plots/png/fastp-seq-quality-plot_Read_1_Before_filtering.png", + "multiqc/multiqc_plots/png/fastp_filtered_reads_plot-cnt.png", + "multiqc/multiqc_plots/png/fastp_filtered_reads_plot-pct.png", "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", @@ -322,6 +348,14 @@ "multiqc/multiqc_plots/svg/bclconvert_sample_counts_Counts_per_lane-pct.svg", "multiqc/multiqc_plots/svg/bclconvert_sample_counts_Index_mismatches-cnt.svg", "multiqc/multiqc_plots/svg/bclconvert_sample_counts_Index_mismatches-pct.svg", + "multiqc/multiqc_plots/svg/fastp-seq-content-gc-plot_Read_1_After_filtering.svg", + "multiqc/multiqc_plots/svg/fastp-seq-content-gc-plot_Read_1_Before_filtering.svg", + "multiqc/multiqc_plots/svg/fastp-seq-content-n-plot_Read_1_After_filtering.svg", + "multiqc/multiqc_plots/svg/fastp-seq-content-n-plot_Read_1_Before_filtering.svg", + "multiqc/multiqc_plots/svg/fastp-seq-quality-plot_Read_1_After_filtering.svg", + "multiqc/multiqc_plots/svg/fastp-seq-quality-plot_Read_1_Before_filtering.svg", + "multiqc/multiqc_plots/svg/fastp_filtered_reads_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastp_filtered_reads_plot-pct.svg", "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", @@ -360,18 +394,24 @@ "SampleSheet.csv:md5,ee5db2e12754e069998b0a96e535238c", "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc", "fastq_list.csv:md5,ae1470cd741e33b87a4ad26f849a50f9", + "Sample1_S1_L001.fastp.json:md5,d9d2d702f3c64412a04cd0768863b1ab", "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", "Sample1_S1_L001_R1_001.fastq.gz.md5:md5,10295d4e5ca66dae7788bbf24886cded", "Sample1_S1_L001_fastqc_data.txt:md5,dc27b3ffca4e60d28ab31bba42bdb551", - "Sample1_S1_L001_report.html:md5,7f1b779da6073fa9626c095f76855840", "Sample1_S1_L001_summary.txt:md5,37bccdcaa1e1fe1022adebf2abad9121", "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "Sample1_S1_L001.samplesheet.csv:md5,fc089e08679ef4559d7cdefbb2a990e6", "bclconvert-lane-stats-table.txt:md5,8bff7b728d3ad67405d4742d0aa2088e", "bclconvert-sample-stats-table.txt:md5,a6edf6b192981bd296c1eba968e4333c", "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", "bclconvert_sample_counts_Counts_per_lane.txt:md5,a7e57ab911ba2cf74ec7bd93b921036d", "bclconvert_sample_counts_Index_mismatches.txt:md5,06c29164e83815c79a2b1541a4a6294e", + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,8105d4ce1d752e1f8a26e4291e8d9c6c", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,0ac68e41c4de8ca35a1cd6ee7c6cb3f3", + "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,1ec69a9fd0d46a39dfb59e377733e98b", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,1ec69a9fd0d46a39dfb59e377733e98b", + "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,1701b40c23dca068210f5410788e3be1", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,35de9aebdc467b1bbc9fd1f40d3aece4", + "fastp_filtered_reads_plot.txt:md5,fa14a1941e109d4104c33db0e5fe20fc", "fastqc-status-check-heatmap.txt:md5,c0a0084f2fbd9d5aa410310ad1906002", "fastqc_per_base_n_content_plot.txt:md5,bc2bc3f88871a2fddf04d8b499fd4e70", "fastqc_per_base_sequence_quality_plot.txt:md5,0d82022063896dabc7ac5beb83a4bc54", @@ -383,21 +423,21 @@ "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", + "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,a894d852b250ee902d805b358c173b88", - "multiqc_general_stats.txt:md5,9e6cd051b09056263f269029b21a643b", - "samplesheet.csv:md5,fc089e08679ef4559d7cdefbb2a990e6" + "multiqc_general_stats.txt:md5,365ea22923184f063b3ad7bd75d7d910" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T10:24:16.70314" + "timestamp": "2024-10-15T11:15:36.996226" }, - "Skip Trimming": { + "Skip MultiQC": { "content": [ - 6, + 5, { "BCLCONVERT": { "bclconvert": "4.3.6" @@ -440,9 +480,101 @@ "220422_M11111_0222_000000000-K9H97/L001/Reports/SampleSheet.csv", "220422_M11111_0222_000000000-K9H97/L001/Reports/Top_Unknown_Barcodes.csv", "220422_M11111_0222_000000000-K9H97/L001/Reports/fastq_list.csv", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz.md5", "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.html", "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.json", "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_fastqc_data.txt", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_report.html", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_summary.txt", + "220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz", + "fastq", + "fastq/Sample1_S1_L001.samplesheet.csv", + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "samplesheet", + "samplesheet/samplesheet.csv" + ], + [ + "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c", + "ControlMetricsOut.bin:md5,6d77b38d0793a6e1ce1e85706e488953", + "CorrectedIntMetricsOut.bin:md5,2bbf84d3be72734addaa2fe794711434", + "ErrorMetricsOut.bin:md5,38c88def138e9bb832539911affdb286", + "ExtractionMetricsOut.bin:md5,7497c3178837eea8f09350b5cd252e99", + "IndexMetricsOut.bin:md5,d41d8cd98f00b204e9800998ecf8427e", + 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"Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", + "Sample1_S1_L001.fastp.json:md5,d9d2d702f3c64412a04cd0768863b1ab", + "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", + "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", + "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", + "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.2" + }, + "timestamp": "2024-10-15T11:20:29.598072" + }, + "Skip Fastp & Fastqc": { + "content": [ + 5, + { + "BCLCONVERT": { + "bclconvert": "4.3.6" + }, + "FALCO": { + "falco": "1.2.1" + }, + "MD5SUM": { + "md5sum": 8.3 + }, + "Workflow": { + "nf-core/demultiplex": "v1.5.2" + } + }, + [ + "220422_M11111_0222_000000000-K9H97", + "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv", + "220422_M11111_0222_000000000-K9H97/InterOp", + "220422_M11111_0222_000000000-K9H97/InterOp/ControlMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/CorrectedIntMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/ErrorMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/ExtractionMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/IndexMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/QMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/InterOp/TileMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/L001", + "220422_M11111_0222_000000000-K9H97/L001/Reports", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Adapter_Cycle_Metrics.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Adapter_Metrics.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Demultiplex_Stats.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Demultiplex_Tile_Stats.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/IndexMetricsOut.bin", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Index_Hopping_Counts.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Quality_Metrics.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Quality_Tile_Metrics.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/RunInfo.xml", + "220422_M11111_0222_000000000-K9H97/L001/Reports/SampleSheet.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/Top_Unknown_Barcodes.csv", + "220422_M11111_0222_000000000-K9H97/L001/Reports/fastq_list.csv", + "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz", "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz.md5", "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_fastqc_data.txt", "220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_report.html", @@ -457,13 +589,6 @@ "multiqc/multiqc_data/bclconvert_lane_counts.txt", "multiqc/multiqc_data/bclconvert_sample_counts_Counts_per_lane.txt", "multiqc/multiqc_data/bclconvert_sample_counts_Index_mismatches.txt", - "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt", - "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt", - "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt", - "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt", - "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt", - "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt", - "multiqc/multiqc_data/fastp_filtered_reads_plot.txt", "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", @@ -478,7 +603,6 @@ "multiqc/multiqc_data/multiqc_bclconvert_bysample.txt", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", - "multiqc/multiqc_data/multiqc_fastp.txt", "multiqc/multiqc_data/multiqc_fastqc.txt", "multiqc/multiqc_data/multiqc_general_stats.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", @@ -493,14 +617,6 @@ "multiqc/multiqc_plots/pdf/bclconvert_sample_counts_Counts_per_lane-pct.pdf", "multiqc/multiqc_plots/pdf/bclconvert_sample_counts_Index_mismatches-cnt.pdf", "multiqc/multiqc_plots/pdf/bclconvert_sample_counts_Index_mismatches-pct.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_After_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_Before_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_1_After_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_1_Before_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_1_After_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_1_Before_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp_filtered_reads_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/fastp_filtered_reads_plot-pct.pdf", "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", @@ -521,14 +637,6 @@ "multiqc/multiqc_plots/png/bclconvert_sample_counts_Counts_per_lane-pct.png", "multiqc/multiqc_plots/png/bclconvert_sample_counts_Index_mismatches-cnt.png", "multiqc/multiqc_plots/png/bclconvert_sample_counts_Index_mismatches-pct.png", - "multiqc/multiqc_plots/png/fastp-seq-content-gc-plot_Read_1_After_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-content-gc-plot_Read_1_Before_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-content-n-plot_Read_1_After_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-content-n-plot_Read_1_Before_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-quality-plot_Read_1_After_filtering.png", - 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"Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", - "Sample1_S1_L001_report.html:md5,194a1a45b6cd90461a1f0d7beee627bb", "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", "Undetermined_S0_L001_R1_001.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "Sample1_S1_L001.samplesheet.csv:md5,7ded6e3f2420a20eb577f930914fd137", "bclconvert-lane-stats-table.txt:md5,8bff7b728d3ad67405d4742d0aa2088e", "bclconvert-sample-stats-table.txt:md5,a6edf6b192981bd296c1eba968e4333c", "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", @@ -236,14 +233,13 @@ "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", - "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4", - "samplesheet.csv:md5,7ded6e3f2420a20eb577f930914fd137" + "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T10:30:20.199021" + "timestamp": "2024-10-15T11:22:30.651976" } } \ No newline at end of file From ba7b97b3973ab4994ea67d4dae10150e6261707b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 13:35:58 +0200 Subject: [PATCH 13/37] update snapshots --- tests/pipeline/bases2fastq.nf.test.snap | 228 +---------- tests/pipeline/bcl2fastq.nf.test.snap | 155 ++++---- tests/pipeline/bclconvert_mini.nf.test.snap | 229 +---------- tests/pipeline/fqtk.nf.test.snap | 228 +---------- tests/pipeline/kraken.nf.test.snap | 18 +- tests/pipeline/mkfastq.nf.test.snap | 311 +++++++-------- tests/pipeline/sgdemux.nf.test.snap | 228 +---------- tests/pipeline/test_pe.nf.test.snap | 405 ++++++++++++-------- 8 files changed, 511 insertions(+), 1291 deletions(-) diff --git a/tests/pipeline/bases2fastq.nf.test.snap b/tests/pipeline/bases2fastq.nf.test.snap index c63ef982..0a69e0cb 100644 --- a/tests/pipeline/bases2fastq.nf.test.snap +++ 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"220422_M11111_0222_000000000-K9H97/L001/Stats/AdapterTrimming.txt", + "220422_M11111_0222_000000000-K9H97/L001/Stats/ConversionStats.xml", + "220422_M11111_0222_000000000-K9H97/L001/Stats/DemultiplexingStats.xml", + "220422_M11111_0222_000000000-K9H97/L001/Stats/DemuxSummaryF1L1.txt", + "220422_M11111_0222_000000000-K9H97/L001/Stats/FastqSummaryF1L1.txt", + "220422_M11111_0222_000000000-K9H97/L001/Stats/Stats.json", "fastq", "fastq/Sample1_S1_L001.samplesheet.csv", "multiqc", "multiqc/multiqc_data", - "multiqc/multiqc_data/bclconvert-lane-stats-table.txt", - "multiqc/multiqc_data/bclconvert-sample-stats-table.txt", - "multiqc/multiqc_data/bclconvert_lane_counts.txt", - "multiqc/multiqc_data/bclconvert_sample_counts_Counts_per_lane.txt", - "multiqc/multiqc_data/bclconvert_sample_counts_Index_mismatches.txt", + "multiqc/multiqc_data/bcl2fastq-lane-stats-table.txt", + "multiqc/multiqc_data/bcl2fastq_lane_counts.txt", + "multiqc/multiqc_data/bcl2fastq_sample_counts.txt", + 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"multiqc/multiqc_plots/pdf/bcl2fastq_undetermined-pct.pdf", "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_After_filtering.pdf", "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_Before_filtering.pdf", "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_1_After_filtering.pdf", @@ -118,14 +134,13 @@ "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/multiqc_plots/pdf/general_stats_table.pdf", "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/bclconvert-lane-stats-table.png", - "multiqc/multiqc_plots/png/bclconvert-sample-stats-table.png", - "multiqc/multiqc_plots/png/bclconvert_lane_counts-cnt.png", - "multiqc/multiqc_plots/png/bclconvert_lane_counts-pct.png", - "multiqc/multiqc_plots/png/bclconvert_sample_counts_Counts_per_lane-cnt.png", - "multiqc/multiqc_plots/png/bclconvert_sample_counts_Counts_per_lane-pct.png", - "multiqc/multiqc_plots/png/bclconvert_sample_counts_Index_mismatches-cnt.png", - 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"multiqc_general_stats.txt:md5,9aed65a87e63b8c0c5f7ef639eea81f3" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T11:04:51.596382" + "timestamp": "2024-10-15T13:14:47.922692" } } \ No newline at end of file diff --git a/tests/pipeline/bclconvert_mini.nf.test.snap b/tests/pipeline/bclconvert_mini.nf.test.snap index 592885cf..46c4a190 100644 --- a/tests/pipeline/bclconvert_mini.nf.test.snap +++ b/tests/pipeline/bclconvert_mini.nf.test.snap @@ -1,245 +1,26 @@ { "BCL-CONVERT-mini": { "content": [ - 6, + 0, { - "BCLCONVERT": { - "bclconvert": "4.3.6" - }, - "FALCO": { - "falco": "1.2.1" - }, - "FASTP": { - "fastp": "0.23.4" - }, - "MD5SUM": { - "md5sum": 8.3 - }, "Workflow": { "nf-core/demultiplex": "v1.5.2" } }, [ - "220422_M11111_0222_000000000-K9H97", - "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv", - "220422_M11111_0222_000000000-K9H97/InterOp", - "220422_M11111_0222_000000000-K9H97/InterOp/ControlMetricsOut.bin", - 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b/tests/pipeline/kraken.nf.test.snap @@ -217,11 +217,11 @@ "QMetricsOut.bin:md5,7e9f198d53ebdfbb699a5f94cf1ed51c", "TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c", "lane.html:md5,794e48287f47a9f22dcb6b6d0c22c3eb", - "laneBarcode.html:md5,b3ee2b3d9b55c0744789e1e73847d8a2", + "laneBarcode.html:md5,600a5f024fea42139b151f7a0ff6f8d3", "lane.html:md5,f741870307050dcea79a838f5971770f", "laneBarcode.html:md5,ffe2e863811c76cb9da27d5d124e0611", - "lane.html:md5,8b58e9ebb82123d09209ad66ddb4e20e", - "laneBarcode.html:md5,8b58e9ebb82123d09209ad66ddb4e20e", + "lane.html:md5,3d9f7881289b00fa6d5e165ed4e4f93d", + "laneBarcode.html:md5,3d9f7881289b00fa6d5e165ed4e4f93d", "lane.html:md5,c383b0768d9978733d3f5d3b91c15af0", "laneBarcode.html:md5,48842c23b9a2816aec540177df870968", "Report.css:md5,eb7d3eb68fc1539f411404987246b59b", @@ -236,15 +236,15 @@ "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", 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a/tests/pipeline/mkfastq.nf.test.snap b/tests/pipeline/mkfastq.nf.test.snap index f25bc158..0aa3c729 100644 --- a/tests/pipeline/mkfastq.nf.test.snap +++ b/tests/pipeline/mkfastq.nf.test.snap @@ -1,13 +1,10 @@ { "MKFASTQ": { "content": [ - 6, + 10, { - "BCLCONVERT": { - "bclconvert": "4.3.6" - }, - "FALCO": { - "falco": "1.2.1" + "CELLRANGER_MKFASTQ": { + "cellranger": "8.0.0" }, "FASTP": { "fastp": "0.23.4" @@ -15,163 +12,150 @@ "MD5SUM": { "md5sum": 8.3 }, + "UNTAR_FLOWCELL": { + "untar": 1.34 + }, "Workflow": { "nf-core/demultiplex": "v1.5.2" } }, [ - "220422_M11111_0222_000000000-K9H97", - "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv", - "220422_M11111_0222_000000000-K9H97/InterOp", - "220422_M11111_0222_000000000-K9H97/InterOp/ControlMetricsOut.bin", - "220422_M11111_0222_000000000-K9H97/InterOp/CorrectedIntMetricsOut.bin", - "220422_M11111_0222_000000000-K9H97/InterOp/ErrorMetricsOut.bin", - "220422_M11111_0222_000000000-K9H97/InterOp/ExtractionMetricsOut.bin", - 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"nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T11:22:30.651976" + "timestamp": "2024-10-15T13:34:19.827174" } } \ No newline at end of file From 41099aac61570016c871711986f360e85d4c200e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 14:30:01 +0200 Subject: [PATCH 14/37] add .nftignore and update snpashots --- tests/pipeline/.nftignore | 8 ++++++++ tests/pipeline/bcl2fastq.nf.test.snap | 16 +--------------- tests/pipeline/kraken.nf.test.snap | 15 +-------------- tests/pipeline/mkfastq.nf.test.snap | 11 ++++------- tests/pipeline/test_pe.nf.test.snap | 17 ++--------------- 5 files changed, 16 insertions(+), 51 deletions(-) diff --git a/tests/pipeline/.nftignore b/tests/pipeline/.nftignore index 923950bc..cc07a136 100644 --- a/tests/pipeline/.nftignore +++ b/tests/pipeline/.nftignore @@ -1,10 +1,18 @@ **/*.fastp.html **/*_report.html +**/Reports/html/**/lane.html +**/Reports/html/**/laneBarcode.html +**/Stats/ConversionStats.xml +**/Stats/DemuxSummaryF1L1.txt +**/Stats/Stats.json fastq/*.samplesheet.csv +multiqc/multiqc_data/bcl2fastq_undetermined.txt multiqc/multiqc_data/multiqc.log +multiqc/multiqc_data/multiqc_bcl2fastq_bylane.txt multiqc/multiqc_data/multiqc_data.json multiqc/multiqc_data/multiqc_software_versions.txt multiqc/multiqc_data/multiqc_sources.txt +multiqc/multiqc_data/multiqc_fastp.txt multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html pipeline_info/*.{html,json,txt,yml} diff --git a/tests/pipeline/bcl2fastq.nf.test.snap b/tests/pipeline/bcl2fastq.nf.test.snap index 7ac77127..f28d843f 100644 --- a/tests/pipeline/bcl2fastq.nf.test.snap +++ b/tests/pipeline/bcl2fastq.nf.test.snap @@ -202,14 +202,6 @@ "IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf", "QMetricsOut.bin:md5,7e9f198d53ebdfbb699a5f94cf1ed51c", "TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c", - "lane.html:md5,794e48287f47a9f22dcb6b6d0c22c3eb", - "laneBarcode.html:md5,b3ee2b3d9b55c0744789e1e73847d8a2", - "lane.html:md5,f741870307050dcea79a838f5971770f", - "laneBarcode.html:md5,ffe2e863811c76cb9da27d5d124e0611", - "lane.html:md5,8b58e9ebb82123d09209ad66ddb4e20e", - "laneBarcode.html:md5,8b58e9ebb82123d09209ad66ddb4e20e", - "lane.html:md5,c383b0768d9978733d3f5d3b91c15af0", - "laneBarcode.html:md5,48842c23b9a2816aec540177df870968", "Report.css:md5,eb7d3eb68fc1539f411404987246b59b", "index.html:md5,5747c407854ae2c358d0ec201ce622d8", "tree.html:md5,a1b9bf592973ca829ec69ddf888b7e34", @@ -220,15 +212,11 @@ "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", "AdapterTrimming.txt:md5,48ed2b914b1246c0b5d8667525550946", - "ConversionStats.xml:md5,a2eaeb8dab2e605db56af05c53855f55", "DemultiplexingStats.xml:md5,2047ff18f5b9107c084de06e9ff943ad", - "DemuxSummaryF1L1.txt:md5,f9782d533f8ac08e2f107f681068c605", "FastqSummaryF1L1.txt:md5,0c6f2d87ee183b84d1051cde9a5643d1", - "Stats.json:md5,199fdf6292e0250385110bebca28b2dc", "bcl2fastq-lane-stats-table.txt:md5,d0e821a9c0ccf7da808c5dd05e99ddc2", "bcl2fastq_lane_counts.txt:md5,9404ab530f43e442093337dd10c351c5", "bcl2fastq_sample_counts.txt:md5,93cb0cd1aee1b464f0e640e1c3d0c142", - "bcl2fastq_undetermined.txt:md5,980cf7e7e430b596392297bc5fc126c7", "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,8105d4ce1d752e1f8a26e4291e8d9c6c", "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,0ac68e41c4de8ca35a1cd6ee7c6cb3f3", "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,1ec69a9fd0d46a39dfb59e377733e98b", @@ -245,10 +233,8 @@ "fastqc_sequence_counts_plot.txt:md5,662c69090978601ca7d39504b1ac736b", "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "multiqc_bcl2fastq_bylane.txt:md5,bde78aa8394c4b7bc4f3cd017e3d29a4", "multiqc_bcl2fastq_bysample.txt:md5,baaa56d8315c18633f6ce6568d6f0657", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", "multiqc_general_stats.txt:md5,9aed65a87e63b8c0c5f7ef639eea81f3" ] @@ -257,6 +243,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T13:14:47.922692" + "timestamp": "2024-10-15T14:28:50.309978" } } \ No newline at end of file diff --git a/tests/pipeline/kraken.nf.test.snap b/tests/pipeline/kraken.nf.test.snap index 62aeda4b..1f82222f 100644 --- a/tests/pipeline/kraken.nf.test.snap +++ b/tests/pipeline/kraken.nf.test.snap @@ -216,14 +216,6 @@ "IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf", "QMetricsOut.bin:md5,7e9f198d53ebdfbb699a5f94cf1ed51c", "TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c", - "lane.html:md5,794e48287f47a9f22dcb6b6d0c22c3eb", - "laneBarcode.html:md5,600a5f024fea42139b151f7a0ff6f8d3", - "lane.html:md5,f741870307050dcea79a838f5971770f", - "laneBarcode.html:md5,ffe2e863811c76cb9da27d5d124e0611", - "lane.html:md5,3d9f7881289b00fa6d5e165ed4e4f93d", - "laneBarcode.html:md5,3d9f7881289b00fa6d5e165ed4e4f93d", - "lane.html:md5,c383b0768d9978733d3f5d3b91c15af0", - "laneBarcode.html:md5,48842c23b9a2816aec540177df870968", "Report.css:md5,eb7d3eb68fc1539f411404987246b59b", "index.html:md5,5747c407854ae2c358d0ec201ce622d8", "tree.html:md5,a1b9bf592973ca829ec69ddf888b7e34", @@ -236,15 +228,11 @@ "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", "AdapterTrimming.txt:md5,48ed2b914b1246c0b5d8667525550946", - "ConversionStats.xml:md5,11f1772e98887151c3d6ee4c7477a4dd", "DemultiplexingStats.xml:md5,2047ff18f5b9107c084de06e9ff943ad", - "DemuxSummaryF1L1.txt:md5,378824327d74ebd3e70ccb359cb6d948", "FastqSummaryF1L1.txt:md5,0c6f2d87ee183b84d1051cde9a5643d1", - "Stats.json:md5,f34d26f0161d8688078c87ffa972b8f9", "bcl2fastq-lane-stats-table.txt:md5,d0e821a9c0ccf7da808c5dd05e99ddc2", "bcl2fastq_lane_counts.txt:md5,9404ab530f43e442093337dd10c351c5", "bcl2fastq_sample_counts.txt:md5,93cb0cd1aee1b464f0e640e1c3d0c142", - "bcl2fastq_undetermined.txt:md5,ea8e5fd28e89828697611a6cad2b7ef6", "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,8105d4ce1d752e1f8a26e4291e8d9c6c", "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,0ac68e41c4de8ca35a1cd6ee7c6cb3f3", "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,1ec69a9fd0d46a39dfb59e377733e98b", @@ -262,7 +250,6 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "kraken-top-n-plot.txt:md5,add0b89a8b3d1729dac311870959b1e7", - "multiqc_bcl2fastq_bylane.txt:md5,b354942bd8f51b11e34816d7c4baf42b", "multiqc_bcl2fastq_bysample.txt:md5,baaa56d8315c18633f6ce6568d6f0657", "multiqc_citations.txt:md5,97f1dcb4348072ce2865c29c5c306a3d", "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", @@ -275,6 +262,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T13:18:26.789525" + "timestamp": "2024-10-15T14:00:41.237358" } } \ No newline at end of file diff --git a/tests/pipeline/mkfastq.nf.test.snap b/tests/pipeline/mkfastq.nf.test.snap index 0aa3c729..0b3f73d9 100644 --- a/tests/pipeline/mkfastq.nf.test.snap +++ b/tests/pipeline/mkfastq.nf.test.snap @@ -167,11 +167,8 @@ "cellranger-tiny-bcl-simple.lane1_no_adapters.csv:md5,86a945ab9d579c7bc98d43f76a07118b", "IndexMetricsOut.bin:md5,e2ac28695537336b53a509f48e93ed1f", "AdapterTrimming.txt:md5,522b8c57ed2a84da31ec3edda9424b60", - "ConversionStats.xml:md5,8e43230be20c13f7a006403ce6f3d128", "DemultiplexingStats.xml:md5,60cce68e6a27371dc257ca9f65e14cc1", - "DemuxSummaryF1L1.txt:md5,ecf4d48c2b6b8cbb68e1facda9a53b43", "FastqSummaryF1L1.txt:md5,876f188644f5e12eca513baeff158306", - "Stats.json:md5,cbf83f5b483d355d0d7cfcaabb41f195", "test_sample_S1_L001.fastp.json:md5,e4321caea21d0c44d0d7269065bdb79d", "test_sample_S1_L001_1.fastp.fastq.gz:md5,b348491a3b1afa096fde514dbdf55215", "test_sample_S1_L001_1.fastp.fastq.gz.md5:md5,43d7882f3aaae47b56df56da6c802236", @@ -180,9 +177,9 @@ { "directory": false, "file": true, - "freeSpace": 21943513088, + "freeSpace": 21964668928, "canonicalPath": "/home/max/workspace/demultiplex/.nf-test/tests/ed2ff7c0bb8147747cb278f737effd34/output/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz", - "usableSpace": 9293074432, + "usableSpace": 9314230272, "hidden": false, "totalSpace": 247570337792, "path": "/home/max/workspace/demultiplex/.nf-test/tests/ed2ff7c0bb8147747cb278f737effd34/output/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz", @@ -213,7 +210,7 @@ "fastp-seq-quality-plot_Read_2_Before_filtering.txt:md5,e80f62d45ca21cacbd19f899f768c308", "fastp_filtered_reads_plot.txt:md5,39d2e637c3e1482821c62c00482c8421", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_fastp.txt:md5,2f4f61ce50ab02186485b57f9d1c5c1b", + "multiqc_fastp.txt:md5,949744c3ef2f89e4a26432cd33307138", "multiqc_general_stats.txt:md5,94b2ad1b21c8f69fd2b57102d52aa7c2" ] ], @@ -221,6 +218,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T13:23:06.229274" + "timestamp": "2024-10-15T14:13:47.87567" } } \ No newline at end of file diff --git a/tests/pipeline/test_pe.nf.test.snap b/tests/pipeline/test_pe.nf.test.snap index d4451301..dc277494 100644 --- a/tests/pipeline/test_pe.nf.test.snap +++ b/tests/pipeline/test_pe.nf.test.snap @@ -264,14 +264,6 @@ [ "PE_Sample.lane1_no_adapters.csv:md5,c31cca10b3a1aed8ec68daf779217d91", "IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf", - "lane.html:md5,eca711b7312a7cf6dd32a6958b2d8812", - "laneBarcode.html:md5,9dcd24a6bf847d2a49b729e6d63f57ba", - "lane.html:md5,41ecd9ef68fc4e1cc3177c23d741428e", - "laneBarcode.html:md5,db047476a60b8dc3b83eb6a9ee77b7db", - "lane.html:md5,849f26ca7c0400b26d81a1a5ce9eaaf6", - "laneBarcode.html:md5,849f26ca7c0400b26d81a1a5ce9eaaf6", - "lane.html:md5,7ea014b0a0c9e9bb1761f291a409f9f0", - "laneBarcode.html:md5,eddae85d4b13d6fb5817df5fbfb756ff", "Report.css:md5,eb7d3eb68fc1539f411404987246b59b", "index.html:md5,5747c407854ae2c358d0ec201ce622d8", "tree.html:md5,a1b9bf592973ca829ec69ddf888b7e34", @@ -287,15 +279,11 @@ "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", "Sample1_S1_L001_R2_001.fastq.gz:md5,146eefcab1eaaef17ffb72672c021368", "AdapterTrimming.txt:md5,8009886a4c060bfec6d8e9346feb0988", - "ConversionStats.xml:md5,633e6e11718bae3d4c966003ec28b2ee", "DemultiplexingStats.xml:md5,2047ff18f5b9107c084de06e9ff943ad", - "DemuxSummaryF1L1.txt:md5,f9782d533f8ac08e2f107f681068c605", "FastqSummaryF1L1.txt:md5,0274549f9541b1ba7828ae6e9c5bcbbd", - "Stats.json:md5,b20fe078247a65fba7142c9b216f26df", "bcl2fastq-lane-stats-table.txt:md5,0c16ec8dd4fdf53afcb6af57272ad92d", "bcl2fastq_lane_counts.txt:md5,d6054e1ec3c2e8d33c3fdee5b250dfbc", "bcl2fastq_sample_counts.txt:md5,93cb0cd1aee1b464f0e640e1c3d0c142", - "bcl2fastq_undetermined.txt:md5,7145a6112f1c0bf556a3b270ea4208c4", "fastp-insert-size-plot.txt:md5,16f66543e78b50ef96e1ef15d0f46087", "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,8105d4ce1d752e1f8a26e4291e8d9c6c", "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,0ac68e41c4de8ca35a1cd6ee7c6cb3f3", @@ -328,7 +316,6 @@ "fastqc-2_sequence_counts_plot.txt:md5,266ea49ebc560e003e3dd1b9f4a21e0d", "fastqc-2_sequence_duplication_levels_plot.txt:md5,02c6dcf1a65b7b3a21d8deaf70c8f3ca", "fastqc-2_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "multiqc_bcl2fastq_bylane.txt:md5,7cf75410bf81ed8a32b7e3d6ebf694f3", "multiqc_bcl2fastq_bysample.txt:md5,bc5b6bbdcd75ead5a552cef09fc9aaec", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", "multiqc_fastp.txt:md5,f5268d082cf1ecf25b16ab66ad7be31c", @@ -341,6 +328,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T13:34:19.827174" + "timestamp": "2024-10-15T14:22:05.629502" } -} \ No newline at end of file +} From 97e509602283ee6b0e4f2ec54681501d997f0d6c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 14:44:30 +0200 Subject: [PATCH 15/37] update snapshots --- tests/pipeline/bclconvert.nf.test.snap | 3 +-- tests/pipeline/kraken.nf.test.snap | 3 +-- tests/pipeline/mkfastq.nf.test.snap | 7 +++---- tests/pipeline/skip_tools.nf.test.snap | 6 ++---- tests/pipeline/test_pe.nf.test.snap | 5 ++--- 5 files changed, 9 insertions(+), 15 deletions(-) diff --git a/tests/pipeline/bclconvert.nf.test.snap b/tests/pipeline/bclconvert.nf.test.snap index c274e21e..ed48b6c5 100644 --- a/tests/pipeline/bclconvert.nf.test.snap +++ b/tests/pipeline/bclconvert.nf.test.snap @@ -231,7 +231,6 @@ "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" ] @@ -240,6 +239,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T11:06:25.196456" + "timestamp": "2024-10-15T14:30:24.488811" } } \ No newline at end of file diff --git a/tests/pipeline/kraken.nf.test.snap b/tests/pipeline/kraken.nf.test.snap index 1f82222f..842970e4 100644 --- a/tests/pipeline/kraken.nf.test.snap +++ b/tests/pipeline/kraken.nf.test.snap @@ -252,7 +252,6 @@ "kraken-top-n-plot.txt:md5,add0b89a8b3d1729dac311870959b1e7", "multiqc_bcl2fastq_bysample.txt:md5,baaa56d8315c18633f6ce6568d6f0657", "multiqc_citations.txt:md5,97f1dcb4348072ce2865c29c5c306a3d", - "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", "multiqc_general_stats.txt:md5,2b86df713f6998ec0468bc4c9a6ec7a3", "multiqc_kraken.txt:md5,a90fd69786a0df1e43b948e423545654" @@ -262,6 +261,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T14:00:41.237358" + "timestamp": "2024-10-15T14:32:46.690205" } } \ No newline at end of file diff --git a/tests/pipeline/mkfastq.nf.test.snap b/tests/pipeline/mkfastq.nf.test.snap index 0b3f73d9..30878dec 100644 --- a/tests/pipeline/mkfastq.nf.test.snap +++ b/tests/pipeline/mkfastq.nf.test.snap @@ -177,9 +177,9 @@ { "directory": false, "file": true, - "freeSpace": 21964668928, + "freeSpace": 19969302528, "canonicalPath": "/home/max/workspace/demultiplex/.nf-test/tests/ed2ff7c0bb8147747cb278f737effd34/output/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz", - "usableSpace": 9314230272, + "usableSpace": 7318863872, "hidden": false, "totalSpace": 247570337792, "path": "/home/max/workspace/demultiplex/.nf-test/tests/ed2ff7c0bb8147747cb278f737effd34/output/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz", @@ -210,7 +210,6 @@ "fastp-seq-quality-plot_Read_2_Before_filtering.txt:md5,e80f62d45ca21cacbd19f899f768c308", "fastp_filtered_reads_plot.txt:md5,39d2e637c3e1482821c62c00482c8421", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_fastp.txt:md5,949744c3ef2f89e4a26432cd33307138", "multiqc_general_stats.txt:md5,94b2ad1b21c8f69fd2b57102d52aa7c2" ] ], @@ -218,6 +217,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T14:13:47.87567" + "timestamp": "2024-10-15T14:34:23.682439" } } \ No newline at end of file diff --git a/tests/pipeline/skip_tools.nf.test.snap b/tests/pipeline/skip_tools.nf.test.snap index 72cc2578..94936415 100644 --- a/tests/pipeline/skip_tools.nf.test.snap +++ b/tests/pipeline/skip_tools.nf.test.snap @@ -424,7 +424,6 @@ "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,a894d852b250ee902d805b358c173b88", "multiqc_general_stats.txt:md5,365ea22923184f063b3ad7bd75d7d910" ] @@ -433,7 +432,7 @@ "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T11:15:36.996226" + "timestamp": "2024-10-15T14:36:31.319794" }, "Skip MultiQC": { "content": [ @@ -959,7 +958,6 @@ "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_fastp.txt:md5,5bce10ca195204bf43b5ef9d17717119", "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" ] @@ -968,6 +966,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T11:18:06.856313" + "timestamp": "2024-10-15T14:38:35.728344" } } \ No newline at end of file diff --git a/tests/pipeline/test_pe.nf.test.snap b/tests/pipeline/test_pe.nf.test.snap index dc277494..dea1698d 100644 --- a/tests/pipeline/test_pe.nf.test.snap +++ b/tests/pipeline/test_pe.nf.test.snap @@ -318,7 +318,6 @@ "fastqc-2_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "multiqc_bcl2fastq_bysample.txt:md5,bc5b6bbdcd75ead5a552cef09fc9aaec", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_fastp.txt:md5,f5268d082cf1ecf25b16ab66ad7be31c", "multiqc_fastqc.txt:md5,c92c8b128147b853b6820ca1025a388c", "multiqc_fastqc_1.txt:md5,5445b6836eaa111b5d4b73bc126afe38", "multiqc_general_stats.txt:md5,2b3479c83a80205dca8db22279aac0fe" @@ -328,6 +327,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T14:22:05.629502" + "timestamp": "2024-10-15T14:42:45.369275" } -} +} \ No newline at end of file From b7fa774e270a0e847213ed9ce35f2737cd8199c3 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 15 Oct 2024 15:46:04 +0200 Subject: [PATCH 16/37] Apply suggestions from code review --- .../local/utils_nfcore_demultiplex_pipeline/main.nf | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf index cc577abb..4c54af7f 100644 --- a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf @@ -97,7 +97,9 @@ workflow PIPELINE_INITIALISATION { } } else { - ch_samplesheet = Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) + ch_samplesheet = Channel + .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) + .map{ validateInputSamplesheet(it) } } emit: @@ -164,6 +166,12 @@ def validateInputParameters() { genomeExistsError() } +// +// Validate channels from input samplesheet +// +def validateInputSamplesheet(input) { + return input +} // // Get attribute from genome config file e.g. fasta // From aa3075273219bfc0539288b0a8545e7b0986af11 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 16:09:15 +0200 Subject: [PATCH 17/37] update snapshots --- tests/pipeline/bases2fastq.nf.test.snap | 217 ++++++- tests/pipeline/fqtk.nf.test.snap | 726 +++++++++++++++++++++- tests/pipeline/sgdemux.nf.test.snap | 776 +++++++++++++++++++++++- 3 files changed, 1703 insertions(+), 16 deletions(-) diff --git a/tests/pipeline/bases2fastq.nf.test.snap b/tests/pipeline/bases2fastq.nf.test.snap index 0a69e0cb..fdaf4200 100644 --- a/tests/pipeline/bases2fastq.nf.test.snap +++ b/tests/pipeline/bases2fastq.nf.test.snap @@ -1,25 +1,232 @@ { "Bases2Fastq": { "content": [ - 0, + 8, { + "BASES2FASTQ": { + "bases2fastq": "1.8.0.1260801529, use subject to license available at elementbiosciences.com" + }, + "FALCO": { + "falco": "1.2.1" + }, + "FASTP": { + "fastp": "0.23.4" + }, + "MD5SUM": { + "md5sum": 8.3 + }, + "UNTAR_FLOWCELL": { + "untar": 1.34 + }, "Workflow": { "nf-core/demultiplex": "v1.5.2" } }, [ + "fastq", + "fastq/DefaultSample.samplesheet.csv", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/fastp-insert-size-plot.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_2_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_2_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_2_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_2_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_2_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_2_Before_filtering.txt", + "multiqc/multiqc_data/fastp_filtered_reads_plot.txt", + "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", + "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_fastp.txt", + "multiqc/multiqc_data/multiqc_fastqc.txt", + "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + 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} -} \ No newline at end of file +} diff --git a/tests/pipeline/sgdemux.nf.test.snap b/tests/pipeline/sgdemux.nf.test.snap index 9aad7757..5675b9bb 100644 --- a/tests/pipeline/sgdemux.nf.test.snap +++ b/tests/pipeline/sgdemux.nf.test.snap @@ -1,25 +1,791 @@ { "SGDEMUX": { "content": [ - 0, + 128, { + "FALCO": { + "falco": "1.2.1" + }, + "FASTP": { + "fastp": "0.23.4" + }, + "MD5SUM": { + "md5sum": 8.3 + }, + "SGDEMUX": { + "sgdemux": "1.1.1" + }, + "UNTAR_FLOWCELL": { + "untar": 1.34 + }, "Workflow": { "nf-core/demultiplex": "v1.5.2" } }, [ + "fastq", + "fastq/Undetermined_S25_L001.samplesheet.csv", + "fastq/s10_S10_L001.samplesheet.csv", + "fastq/s11_S11_L001.samplesheet.csv", + "fastq/s12_S12_L001.samplesheet.csv", + "fastq/s13_S13_L001.samplesheet.csv", + "fastq/s14_S14_L001.samplesheet.csv", + "fastq/s15_S15_L001.samplesheet.csv", + "fastq/s16_S16_L001.samplesheet.csv", + "fastq/s17_S17_L001.samplesheet.csv", + "fastq/s18_S18_L001.samplesheet.csv", + 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"s7_S7_L001_2.fastp.fastq.gz:md5,25c2c1055b85d8428bd9b4631ea3a77b", + "s7_S7_L001_2.fastp.fastq.gz.md5:md5,b919aa857d42280c5ba0f9732ae4cc23", + "s7_S7_L001_2.fastp.fastq.gz_fastqc_data.txt:md5,07a28fe6179ab8bbf8562dc57f9c5a76", + "s7_S7_L001_2.fastp.fastq.gz_summary.txt:md5,1e7ec6e822f8a6332b7b7c2e8b4e6452", + "s8_S8_L001.fastp.json:md5,5bfcfe29a43c0d0ba8fac7fc9f084f04", + "s8_S8_L001_1.fastp.fastq.gz:md5,e4582608f01a4b61709f64e11981754c", + "s8_S8_L001_1.fastp.fastq.gz.md5:md5,36eb0b921149cdadb4b134a7ad3027ea", + "s8_S8_L001_1.fastp.fastq.gz_fastqc_data.txt:md5,72bbd7b369881b2c19bc36fce1560e86", + "s8_S8_L001_1.fastp.fastq.gz_summary.txt:md5,6ca5a53521272529d40149e0a0e78eec", + "s8_S8_L001_2.fastp.fastq.gz:md5,aea4d16c6afb9cc26cfb3b87f750fd4a", + "s8_S8_L001_2.fastp.fastq.gz.md5:md5,2c880372773ce9ef5a01a410c075fdef", + "s8_S8_L001_2.fastp.fastq.gz_fastqc_data.txt:md5,c6cb60dbcb95f28ac2d851d44e45f4d1", + "s8_S8_L001_2.fastp.fastq.gz_summary.txt:md5,5bbac0dc1a786404657e3824d383c36d", + "s9_S9_L001.fastp.json:md5,709a327e837b44dc186c3407b91ab9c4", + "s9_S9_L001_1.fastp.fastq.gz:md5,e7b31d4bde7b64f5513e1ab881fc62e1", + "s9_S9_L001_1.fastp.fastq.gz.md5:md5,c53eab213c0f4102b8b521095134c641", + "s9_S9_L001_1.fastp.fastq.gz_fastqc_data.txt:md5,5ab4a18d6b25c024be571ae67a918851", + "s9_S9_L001_1.fastp.fastq.gz_summary.txt:md5,637f54a93198ba85537bcf73acd69895", + "s9_S9_L001_2.fastp.fastq.gz:md5,7da27e3357d8642ebfc1665b7e99be68", + "s9_S9_L001_2.fastp.fastq.gz.md5:md5,aef2fa5b73b4a08410ba084e52563687", + "s9_S9_L001_2.fastp.fastq.gz_fastqc_data.txt:md5,956862e3eb6abf519ddf5fa6c92c0c79", + "s9_S9_L001_2.fastp.fastq.gz_summary.txt:md5,7dc0d8335349100658abbcaaa1dcdf35", + "sample_barcode_hop_metrics.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T13:24:08.410697" + "timestamp": "2024-10-15T16:07:45.042862" } } \ No newline at end of file From 3a42ad4b83f8c44e97facf664dd4a5ffab91d62f Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 15 Oct 2024 17:47:12 +0200 Subject: [PATCH 18/37] Update conf/test_full.config --- conf/test_full.config | 9 --------- 1 file changed, 9 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index 3761c534..40209e9a 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,15 +10,6 @@ ---------------------------------------------------------------------------------------- */ -// Limit resources so that this can run on GitHub Actions -process { - resourceLimits = [ - cpus: 4, - memory: '15.GB', - time: '1.h' - ] -} - params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' From a99af46903c9c5217ea8f6fdf30ea072a57ca7df Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 16:17:12 +0200 Subject: [PATCH 19/37] code polish --- subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf index 4c54af7f..13011ae2 100644 --- a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf @@ -68,7 +68,6 @@ workflow PIPELINE_INITIALISATION { // validateInputParameters() - // // Create channel from input file provided through params.input // From e235b22f5a59cfdf3bec49e737e4b3140f266f22 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 16:37:05 +0200 Subject: [PATCH 20/37] code polish --- main.nf | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/main.nf b/main.nf index db23cb52..d7dcc41e 100755 --- a/main.nf +++ b/main.nf @@ -15,18 +15,9 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { DEMULTIPLEX } from './workflows/demultiplex' -include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_demultiplex_pipeline' +include { DEMULTIPLEX } from './workflows/demultiplex' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_demultiplex_pipeline' -include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_demultiplex_pipeline' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - - +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_demultiplex_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -50,6 +41,7 @@ workflow NFCORE_DEMULTIPLEX { DEMULTIPLEX ( samplesheet ) + emit: multiqc_report = DEMULTIPLEX.out.multiqc_report // channel: /path/to/multiqc_report.html } @@ -78,6 +70,7 @@ workflow { NFCORE_DEMULTIPLEX ( PIPELINE_INITIALISATION.out.samplesheet ) + // // SUBWORKFLOW: Run completion tasks // From bdbbb4c2da9c170545e47c4fd3d5fbadde3fbe08 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 16:37:12 +0200 Subject: [PATCH 21/37] fix join --- workflows/demultiplex.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflows/demultiplex.nf b/workflows/demultiplex.nf index c1f1b3fe..8177c52f 100644 --- a/workflows/demultiplex.nf +++ b/workflows/demultiplex.nf @@ -50,6 +50,7 @@ workflow DEMULTIPLEX { take: ch_samplesheet // channel: samplesheet read in from --input + main: // Value inputs demultiplexer = params.demultiplexer // string: bases2fastq, bcl2fastq, bclconvert, fqtk, sgdemux, mkfastq @@ -75,7 +76,7 @@ workflow DEMULTIPLEX { } .map { file -> //build meta again from file name def meta_id = (file =~ /.*\/(.*?)(\.lane|_no_adapters)/)[0][1] //extracts everything from the last "/" until ".lane" or "_no_adapters" - def meta_lane = (file.getName().contains('.lane')) ? (file =~ /\.lane(\d+)/)[0][1].toInteger() : null //extracts number after ".lane" until next "_", must be int to match lane value from meta + def meta_lane = (file.getName().contains('.lane')) ? (file =~ /\.lane(\d+)/)[0][1].toInteger() : [] //extracts number after ".lane" until next "_", must be int to match lane value from meta [[id: meta_id, lane: meta_lane],file] } ch_samplesheet_new = ch_samplesheet From f622cb2bac9921cddf98306b5fd5734f414f097b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 16:37:18 +0200 Subject: [PATCH 22/37] update .nftignore --- tests/pipeline/.nftignore | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/tests/pipeline/.nftignore b/tests/pipeline/.nftignore index cc07a136..6453b710 100644 --- a/tests/pipeline/.nftignore +++ b/tests/pipeline/.nftignore @@ -10,10 +10,15 @@ multiqc/multiqc_data/bcl2fastq_undetermined.txt multiqc/multiqc_data/multiqc.log multiqc/multiqc_data/multiqc_bcl2fastq_bylane.txt multiqc/multiqc_data/multiqc_data.json +multiqc/multiqc_data/multiqc_fastp.txt +multiqc/multiqc_data/multiqc_fastqc.txt +multiqc/multiqc_data/multiqc_fastqc_*.txt multiqc/multiqc_data/multiqc_software_versions.txt multiqc/multiqc_data/multiqc_sources.txt -multiqc/multiqc_data/multiqc_fastp.txt multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html pipeline_info/*.{html,json,txt,yml} samplesheet/samplesheet.csv +sim-data/*.fastp.fastq.gz +sim-data/*.fastp.fastq.gz.md5 +sim-data/most_frequent_unmatched.tsv From c832ffbd7cc5076bbcc0b292800097ae990974f1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 17:02:41 +0200 Subject: [PATCH 23/37] no need for functions test since function was removed in 1.5.0 --- tests/functions/demultiplex.nf.test | 35 ------------------------ tests/functions/demultiplex.nf.test.snap | 6 ---- 2 files changed, 41 deletions(-) delete mode 100644 tests/functions/demultiplex.nf.test delete mode 100644 tests/functions/demultiplex.nf.test.snap diff --git a/tests/functions/demultiplex.nf.test b/tests/functions/demultiplex.nf.test deleted file mode 100644 index 97c42247..00000000 --- a/tests/functions/demultiplex.nf.test +++ /dev/null @@ -1,35 +0,0 @@ -nextflow_function { - - name "Test Functions" - script "workflows/demultiplex.nf" - - // TODO test("Test Function summary_params = NfcoreSchema.paramsSummaryMap") - - test("Test Function extract_csv") { - - function "extract_csv" - - when { - function { - """ - input[0] = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv' - """ - } - } - - then { - // FIXME - assert function.failed - assert snapshot(function.result).match() - } - - } - - // TODO test("Test Function all_columns = input_schema.columns.keySet().collect") - // TODO test("Test Function commons = all_columns.intersect") - // TODO test("Test Function diffs = all_columns.plus") - // TODO test("Test Function parse_flowcell_csv") - // TODO test("Test Function flowcell = file") - // TODO test("Test Function samplesheet = file") - -} diff --git a/tests/functions/demultiplex.nf.test.snap b/tests/functions/demultiplex.nf.test.snap deleted file mode 100644 index 81b1a55b..00000000 --- a/tests/functions/demultiplex.nf.test.snap +++ /dev/null @@ -1,6 +0,0 @@ -{ - "Test Function extract_csv": { - "content": null, - "timestamp": "2023-06-05T10:39:32+0000" - } -} \ No newline at end of file From 39694d44ab3ab13011de0a2358f62e882bb1655a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 17:06:13 +0200 Subject: [PATCH 24/37] all tests are pipeline tests --- tests/{pipeline => }/.nftignore | 0 tests/{pipeline => }/bases2fastq.nf.test | 4 +- ....nf.test.snap => bases2fastq.nf.test.snap} | 7 +- tests/{pipeline => }/bcl2fastq.nf.test | 4 +- tests/{pipeline => }/bcl2fastq.nf.test.snap | 3 +- tests/{pipeline => }/bclconvert.nf.test | 4 +- tests/{pipeline => }/bclconvert.nf.test.snap | 3 +- tests/{pipeline => }/bclconvert_mini.nf.test | 4 +- tests/bclconvert_mini.nf.test.snap | 356 +++++++++ tests/{pipeline => }/fqtk.nf.test | 4 +- tests/fqtk.nf.test.snap | 25 + tests/{pipeline => }/kraken.nf.test | 4 +- tests/{pipeline => }/kraken.nf.test.snap | 3 +- tests/{pipeline => }/mkfastq.nf.test | 4 +- tests/{pipeline => }/mkfastq.nf.test.snap | 0 tests/pipeline/bases2fastq.nf.test.snap | 232 ------ tests/pipeline/fqtk.nf.test.snap | 739 ------------------ tests/{pipeline => }/sgdemux.nf.test | 4 +- tests/{pipeline => }/sgdemux.nf.test.snap | 2 +- tests/{pipeline => }/skip_tools.nf.test | 12 +- tests/{pipeline => }/skip_tools.nf.test.snap | 0 tests/{pipeline => }/test_pe.nf.test | 4 +- tests/{pipeline => }/test_pe.nf.test.snap | 0 23 files changed, 412 insertions(+), 1006 deletions(-) rename tests/{pipeline => }/.nftignore (100%) rename tests/{pipeline => }/bases2fastq.nf.test (95%) rename tests/{pipeline/bclconvert_mini.nf.test.snap => bases2fastq.nf.test.snap} (68%) rename tests/{pipeline => }/bcl2fastq.nf.test (95%) rename tests/{pipeline => }/bcl2fastq.nf.test.snap (99%) rename tests/{pipeline => }/bclconvert.nf.test (95%) rename tests/{pipeline => }/bclconvert.nf.test.snap (99%) rename tests/{pipeline => }/bclconvert_mini.nf.test (95%) create mode 100644 tests/bclconvert_mini.nf.test.snap rename tests/{pipeline => }/fqtk.nf.test (95%) create mode 100644 tests/fqtk.nf.test.snap rename tests/{pipeline => }/kraken.nf.test (96%) rename tests/{pipeline => }/kraken.nf.test.snap (99%) rename tests/{pipeline => }/mkfastq.nf.test (95%) rename tests/{pipeline => }/mkfastq.nf.test.snap (100%) delete mode 100644 tests/pipeline/bases2fastq.nf.test.snap delete mode 100644 tests/pipeline/fqtk.nf.test.snap rename tests/{pipeline => }/sgdemux.nf.test (95%) rename tests/{pipeline => }/sgdemux.nf.test.snap (99%) rename tests/{pipeline => }/skip_tools.nf.test (97%) rename tests/{pipeline => }/skip_tools.nf.test.snap (100%) rename tests/{pipeline => }/test_pe.nf.test (95%) rename tests/{pipeline => }/test_pe.nf.test.snap (100%) diff --git a/tests/pipeline/.nftignore b/tests/.nftignore similarity index 100% rename from tests/pipeline/.nftignore rename to tests/.nftignore diff --git a/tests/pipeline/bases2fastq.nf.test b/tests/bases2fastq.nf.test similarity index 95% rename from tests/pipeline/bases2fastq.nf.test rename to tests/bases2fastq.nf.test index 71584e64..71de1afb 100644 --- a/tests/pipeline/bases2fastq.nf.test +++ b/tests/bases2fastq.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test Workflow main.nf - BASES2FASTQ" - script "main.nf" + script "../main.nf" profile "test_bases2fastq" tag "bases2fastq" tag "pipeline" @@ -18,7 +18,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/bclconvert_mini.nf.test.snap b/tests/bases2fastq.nf.test.snap similarity index 68% rename from tests/pipeline/bclconvert_mini.nf.test.snap rename to tests/bases2fastq.nf.test.snap index 46c4a190..52d3fbda 100644 --- a/tests/pipeline/bclconvert_mini.nf.test.snap +++ b/tests/bases2fastq.nf.test.snap @@ -1,5 +1,5 @@ { - "BCL-CONVERT-mini": { + "Bases2Fastq": { "content": [ 0, { @@ -8,19 +8,18 @@ } }, [ - "miniseq_truseq_smrna_no_adapters.csv", "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet" ], [ - "miniseq_truseq_smrna_no_adapters.csv:md5,c32433167a5c56d5c15952c2e7948898" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T13:16:42.877259" + "timestamp": "2024-10-15T16:37:55.855747" } } \ No newline at end of file diff --git a/tests/pipeline/bcl2fastq.nf.test b/tests/bcl2fastq.nf.test similarity index 95% rename from tests/pipeline/bcl2fastq.nf.test rename to tests/bcl2fastq.nf.test index 4719cdde..ef69097b 100644 --- a/tests/pipeline/bcl2fastq.nf.test +++ b/tests/bcl2fastq.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test Workflow main.nf - BCL2FASTQ" - script "main.nf" + script "../main.nf" profile "test_bcl2fastq" tag "bcl2fastq" tag "pipeline" @@ -18,7 +18,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/bcl2fastq.nf.test.snap b/tests/bcl2fastq.nf.test.snap similarity index 99% rename from tests/pipeline/bcl2fastq.nf.test.snap rename to tests/bcl2fastq.nf.test.snap index f28d843f..a52d8832 100644 --- a/tests/pipeline/bcl2fastq.nf.test.snap +++ b/tests/bcl2fastq.nf.test.snap @@ -235,7 +235,6 @@ "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "multiqc_bcl2fastq_bysample.txt:md5,baaa56d8315c18633f6ce6568d6f0657", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", "multiqc_general_stats.txt:md5,9aed65a87e63b8c0c5f7ef639eea81f3" ] ], @@ -243,6 +242,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T14:28:50.309978" + "timestamp": "2024-10-15T16:39:25.304794" } } \ No newline at end of file diff --git a/tests/pipeline/bclconvert.nf.test b/tests/bclconvert.nf.test similarity index 95% rename from tests/pipeline/bclconvert.nf.test rename to tests/bclconvert.nf.test index 9971db94..efdc72c1 100644 --- a/tests/pipeline/bclconvert.nf.test +++ b/tests/bclconvert.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test Workflow main.nf - BCLCONVERT" - script "main.nf" + script "../main.nf" profile "test" tag "bclconvert" tag "pipeline" @@ -18,7 +18,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/bclconvert.nf.test.snap b/tests/bclconvert.nf.test.snap similarity index 99% rename from tests/pipeline/bclconvert.nf.test.snap rename to tests/bclconvert.nf.test.snap index ed48b6c5..3145a5ac 100644 --- a/tests/pipeline/bclconvert.nf.test.snap +++ b/tests/bclconvert.nf.test.snap @@ -231,7 +231,6 @@ "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" ] ], @@ -239,6 +238,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T14:30:24.488811" + "timestamp": "2024-10-15T16:41:01.01928" } } \ No newline at end of file diff --git a/tests/pipeline/bclconvert_mini.nf.test b/tests/bclconvert_mini.nf.test similarity index 95% rename from tests/pipeline/bclconvert_mini.nf.test rename to tests/bclconvert_mini.nf.test index 82fc94b3..19f24167 100644 --- a/tests/pipeline/bclconvert_mini.nf.test +++ b/tests/bclconvert_mini.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test Workflow main.nf - BCLCONVERT-mini" - script "main.nf" + script "../main.nf" profile "test_bclconvert" tag "bclconvert" tag "pipeline" @@ -18,7 +18,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/bclconvert_mini.nf.test.snap b/tests/bclconvert_mini.nf.test.snap new file mode 100644 index 00000000..1964ed33 --- /dev/null +++ b/tests/bclconvert_mini.nf.test.snap @@ -0,0 +1,356 @@ +{ + "BCL-CONVERT-mini": { + "content": [ + 26, + { + "BCLCONVERT": { + "bclconvert": "4.3.6" + }, + "FALCO": { + "falco": 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FQTK" - script "main.nf" + script "../main.nf" profile "test_fqtk" tag "fqtk" @@ -17,7 +17,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/fqtk.nf.test.snap b/tests/fqtk.nf.test.snap new file mode 100644 index 00000000..f4d2401f --- /dev/null +++ b/tests/fqtk.nf.test.snap @@ -0,0 +1,25 @@ +{ + "FQTK": { + "content": [ + 0, + { + "Workflow": { + "nf-core/demultiplex": "v1.5.2" + } + }, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "samplesheet" + ], + [ + + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.2" + }, + "timestamp": "2024-10-15T16:56:01.494868" + } +} \ No newline at end of file diff --git a/tests/pipeline/kraken.nf.test b/tests/kraken.nf.test similarity index 96% rename from tests/pipeline/kraken.nf.test rename to tests/kraken.nf.test index 614b6e18..3f050e9d 100644 --- a/tests/pipeline/kraken.nf.test +++ b/tests/kraken.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test Workflow main.nf - Kraken" - script "main.nf" + script "../main.nf" config "../../conf/test_kraken.config" profile "test" tag "kraken" @@ -24,7 +24,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/kraken.nf.test.snap b/tests/kraken.nf.test.snap similarity index 99% rename from tests/pipeline/kraken.nf.test.snap rename to tests/kraken.nf.test.snap index 842970e4..8d1fa326 100644 --- a/tests/pipeline/kraken.nf.test.snap +++ b/tests/kraken.nf.test.snap @@ -252,7 +252,6 @@ "kraken-top-n-plot.txt:md5,add0b89a8b3d1729dac311870959b1e7", "multiqc_bcl2fastq_bysample.txt:md5,baaa56d8315c18633f6ce6568d6f0657", "multiqc_citations.txt:md5,97f1dcb4348072ce2865c29c5c306a3d", - "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", "multiqc_general_stats.txt:md5,2b86df713f6998ec0468bc4c9a6ec7a3", "multiqc_kraken.txt:md5,a90fd69786a0df1e43b948e423545654" ] @@ -261,6 +260,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T14:32:46.690205" + "timestamp": "2024-10-15T16:57:22.70902" } } \ No newline at end of file diff --git a/tests/pipeline/mkfastq.nf.test b/tests/mkfastq.nf.test similarity index 95% rename from tests/pipeline/mkfastq.nf.test rename to tests/mkfastq.nf.test index 18efa05c..a9378098 100644 --- a/tests/pipeline/mkfastq.nf.test +++ b/tests/mkfastq.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test Workflow main.nf - mkfastq" - script "main.nf" + script "../main.nf" profile "test_mkfastq" tag "mkfastq" tag "pipeline" @@ -18,7 +18,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/mkfastq.nf.test.snap b/tests/mkfastq.nf.test.snap similarity index 100% rename from tests/pipeline/mkfastq.nf.test.snap rename to tests/mkfastq.nf.test.snap diff --git a/tests/pipeline/bases2fastq.nf.test.snap b/tests/pipeline/bases2fastq.nf.test.snap deleted file mode 100644 index fdaf4200..00000000 --- a/tests/pipeline/bases2fastq.nf.test.snap +++ /dev/null @@ -1,232 +0,0 @@ -{ - "Bases2Fastq": { - "content": [ - 8, - { - "BASES2FASTQ": { - "bases2fastq": "1.8.0.1260801529, use subject to license available at elementbiosciences.com" - }, - "FALCO": { - "falco": "1.2.1" - }, - "FASTP": { - "fastp": "0.23.4" - }, - "MD5SUM": { - "md5sum": 8.3 - }, - "UNTAR_FLOWCELL": { - "untar": 1.34 - }, - "Workflow": { - "nf-core/demultiplex": "v1.5.2" - } - }, - [ - "fastq", - "fastq/DefaultSample.samplesheet.csv", - "multiqc", - "multiqc/multiqc_data", - "multiqc/multiqc_data/fastp-insert-size-plot.txt", - 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"s5_1.fastp.fastq.gz:md5,2c111ddbdc64a9f4a9fc7a27f2e2aaea", - "s5_1.fastp.fastq.gz.md5:md5,7fffdc9a1785f132cf56800a269aa20d", - "s5_1.fastp.fastq.gz_fastqc_data.txt:md5,c54f90f7b4623bd3bdfe8580b277af0b", - "s5_1.fastp.fastq.gz_summary.txt:md5,cd6ae5046c4bef89115a98fc3b6a1282", - "s5_2.fastp.fastq.gz:md5,6ae8e46cf5fa66f6998a72f15caa9c58", - "s5_2.fastp.fastq.gz.md5:md5,bb1dfb34b2cfb26b5dbef8493eb4fdfe", - "s5_2.fastp.fastq.gz_fastqc_data.txt:md5,9df4fa82eb11393fb57d7c029c7ae327", - "s5_2.fastp.fastq.gz_summary.txt:md5,2fe1f212327441aa271f7f308270f3d2", - "s6.fastp.json:md5,6a0c0339fed4eb4f7e5780b7fef079d2", - "s6_1.fastp.fastq.gz:md5,cc6c0fb00166827307c846c8e9661c47", - "s6_1.fastp.fastq.gz.md5:md5,81910b3afe48abf930d7623f94adf9f6", - "s6_1.fastp.fastq.gz_fastqc_data.txt:md5,f6dcd4caa543e6b9bd7f683c50d09a84", - "s6_1.fastp.fastq.gz_summary.txt:md5,babe9aa8373d25fd029fd0bd4c1bcdc2", - "s6_2.fastp.fastq.gz:md5,6d5556ca178aab7202cf860fff94f574", - "s6_2.fastp.fastq.gz.md5:md5,2417e2f3c914fa8f032afd8676b2d43d", - "s6_2.fastp.fastq.gz_fastqc_data.txt:md5,a0cfd6e5c6d000b54798aa7967b654d5", - "s6_2.fastp.fastq.gz_summary.txt:md5,1afa3915b57e51d56eb998af0c2121a8", - "s7.fastp.json:md5,19d4c1d93cfddfe31c5be76dc0e1b50a", - "s7_1.fastp.fastq.gz:md5,36ab856e02e7d1c17c3a122ec9179cbb", - "s7_1.fastp.fastq.gz.md5:md5,6942c45c37a57407853cfcbef1a7576e", - "s7_1.fastp.fastq.gz_fastqc_data.txt:md5,a8f1a1249da32dc1bafe64ef11ff333e", - "s7_1.fastp.fastq.gz_summary.txt:md5,5ff0936a3b19a6cba43d74c59a4ffbfa", - "s7_2.fastp.fastq.gz:md5,0764aae83716030f4ea05cca5d4511a4", - "s7_2.fastp.fastq.gz.md5:md5,08bbbd69fc3ee7df14b33947f3265790", - "s7_2.fastp.fastq.gz_fastqc_data.txt:md5,4eda9a3f2a829184adbb61fcea58f6b4", - "s7_2.fastp.fastq.gz_summary.txt:md5,5d47846f21b5fe4e8b05cdd054f6a91b", - "s8.fastp.json:md5,bad705ea8bbd9957d3a1bb831b2966c2", - "s8_1.fastp.fastq.gz:md5,f37f97582eafb96aae79a1d635e4585e", - "s8_1.fastp.fastq.gz.md5:md5,530292bf972cf1b4b234fc40ae40e402", - "s8_1.fastp.fastq.gz_fastqc_data.txt:md5,9769a7bce94f65c7eb7d0a64f00607b5", - "s8_1.fastp.fastq.gz_summary.txt:md5,a65831285ff1b417c72dd20fe7393ad0", - "s8_2.fastp.fastq.gz:md5,b5e48a29663e3e92354794290e2ba419", - "s8_2.fastp.fastq.gz.md5:md5,ec862cc5d2cc18be996a8a38b4052d87", - "s8_2.fastp.fastq.gz_fastqc_data.txt:md5,065d4208b7d2c0162b71e47a673b6cd7", - "s8_2.fastp.fastq.gz_summary.txt:md5,821bbcf71f1e5e568aee2e8ac5788305", - "s9.fastp.json:md5,a961c9be7ef88ae4bc188809d6383842", - "s9_1.fastp.fastq.gz:md5,42e79f8a4e8db043b76782538982d1ea", - "s9_1.fastp.fastq.gz.md5:md5,9ba7d8112363ed1de4e542e458ad02fa", - "s9_1.fastp.fastq.gz_fastqc_data.txt:md5,861216d8769fcf246198ce71e550c50d", - "s9_1.fastp.fastq.gz_summary.txt:md5,47a130225685bbfde4f1f0a285a1f380", - "s9_2.fastp.fastq.gz:md5,d3af5fce6432934a479770f16c8f50b1", - "s9_2.fastp.fastq.gz.md5:md5,35b322363f80b060c3c79b6d21448661", - "s9_2.fastp.fastq.gz_fastqc_data.txt:md5,44ac3768c508a14eea3756ed88271d96", - "s9_2.fastp.fastq.gz_summary.txt:md5,d6c912c1a073a7b0df9c1c3e00b1b814", - "unmatched.fastp.json:md5,4f4f375bc6fef5880d843df77ae2d5f1", - "unmatched_1.fastp.fastq.gz:md5,8f77e8d5adc4b16dd499fe3bd092f66d", - "unmatched_1.fastp.fastq.gz.md5:md5,5b5876132b859c7dc6558bc63b24f8bf", - "unmatched_1.fastp.fastq.gz_fastqc_data.txt:md5,03d2a927a8850e90f4401c5e7cb469ec", - "unmatched_1.fastp.fastq.gz_summary.txt:md5,8f82f5c293be99943424dd66ebc74627", - "unmatched_2.fastp.fastq.gz:md5,a2c623dcaa11fe3faaecc563c376f24b", - "unmatched_2.fastp.fastq.gz.md5:md5,ea51457970db5e6690a0f76cd2b6be85", - "unmatched_2.fastp.fastq.gz_fastqc_data.txt:md5,ba1ff6c0e111ebdb3a269a3add145ae6", - "unmatched_2.fastp.fastq.gz_summary.txt:md5,202c2d50118198e29ead032008eab7d6" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-15T16:04:44.041642" - } -} diff --git a/tests/pipeline/sgdemux.nf.test b/tests/sgdemux.nf.test similarity index 95% rename from tests/pipeline/sgdemux.nf.test rename to tests/sgdemux.nf.test index 93f22c91..7fa83e77 100644 --- a/tests/pipeline/sgdemux.nf.test +++ b/tests/sgdemux.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test Workflow main.nf - Sgdemux" - script "main.nf" + script "../main.nf" profile "test_sgdemux" tag "sgdemux" tag "pipeline" @@ -18,7 +18,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/sgdemux.nf.test.snap b/tests/sgdemux.nf.test.snap similarity index 99% rename from tests/pipeline/sgdemux.nf.test.snap rename to tests/sgdemux.nf.test.snap index 5675b9bb..711cf84f 100644 --- a/tests/pipeline/sgdemux.nf.test.snap +++ b/tests/sgdemux.nf.test.snap @@ -788,4 +788,4 @@ }, "timestamp": "2024-10-15T16:07:45.042862" } -} \ No newline at end of file +} diff --git a/tests/pipeline/skip_tools.nf.test b/tests/skip_tools.nf.test similarity index 97% rename from tests/pipeline/skip_tools.nf.test rename to tests/skip_tools.nf.test index 9a388def..938abc67 100644 --- a/tests/pipeline/skip_tools.nf.test +++ b/tests/skip_tools.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test Workflow main.nf - Skip Tools" - script "main.nf" + script "../main.nf" profile "test" tag "skip_trimming" tag "pipeline" @@ -22,7 +22,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -54,7 +54,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -86,7 +86,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -118,7 +118,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -150,7 +150,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/skip_tools.nf.test.snap b/tests/skip_tools.nf.test.snap similarity index 100% rename from tests/pipeline/skip_tools.nf.test.snap rename to tests/skip_tools.nf.test.snap diff --git a/tests/pipeline/test_pe.nf.test b/tests/test_pe.nf.test similarity index 95% rename from tests/pipeline/test_pe.nf.test rename to tests/test_pe.nf.test index 1663c0d6..9382ea56 100644 --- a/tests/pipeline/test_pe.nf.test +++ b/tests/test_pe.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test Workflow main.nf - Test PE" - script "main.nf" + script "../main.nf" profile "test_pe" tag "bcl2fastq_pe" tag "pipeline" @@ -18,7 +18,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/pipeline/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/pipeline/test_pe.nf.test.snap b/tests/test_pe.nf.test.snap similarity index 100% rename from tests/pipeline/test_pe.nf.test.snap rename to tests/test_pe.nf.test.snap From 429c20b3f332ffbe809154ea3baeac5d674a7b2a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 17:12:52 +0200 Subject: [PATCH 25/37] do we really need this file? --- subworkflows/local/.gitkeep | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 subworkflows/local/.gitkeep diff --git a/subworkflows/local/.gitkeep b/subworkflows/local/.gitkeep deleted file mode 100644 index e69de29b..00000000 From 80dd819244804a6ea17ecc33161b0b9347cb7771 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 18:35:47 +0200 Subject: [PATCH 26/37] code polish --- .../local/utils_nfcore_demultiplex_pipeline/main.nf | 9 +-------- workflows/demultiplex.nf | 8 ++++---- 2 files changed, 5 insertions(+), 12 deletions(-) diff --git a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf index 13011ae2..35008413 100644 --- a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf @@ -84,7 +84,7 @@ workflow PIPELINE_INITIALISATION { if ( !file(per_flowcell_manifest).exists() ){ error "[Samplesheet Error] The per flowcell manifest file does not exist: ${per_flowcell_manifest}" } - [meta, samplesheet, flowcell, per_flowcell_manifest] + [ meta, samplesheet, flowcell, per_flowcell_manifest ] } ch_flowcell_manifest = ch_samplesheet.map{ meta, samplesheet, flowcell, per_flowcell_manifest -> per_flowcell_manifest } @@ -98,7 +98,6 @@ workflow PIPELINE_INITIALISATION { } else { ch_samplesheet = Channel .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) - .map{ validateInputSamplesheet(it) } } emit: @@ -165,12 +164,6 @@ def validateInputParameters() { genomeExistsError() } -// -// Validate channels from input samplesheet -// -def validateInputSamplesheet(input) { - return input -} // // Get attribute from genome config file e.g. fasta // diff --git a/workflows/demultiplex.nf b/workflows/demultiplex.nf index 8177c52f..7595afd1 100644 --- a/workflows/demultiplex.nf +++ b/workflows/demultiplex.nf @@ -76,12 +76,12 @@ workflow DEMULTIPLEX { } .map { file -> //build meta again from file name def meta_id = (file =~ /.*\/(.*?)(\.lane|_no_adapters)/)[0][1] //extracts everything from the last "/" until ".lane" or "_no_adapters" - def meta_lane = (file.getName().contains('.lane')) ? (file =~ /\.lane(\d+)/)[0][1].toInteger() : [] //extracts number after ".lane" until next "_", must be int to match lane value from meta - [[id: meta_id, lane: meta_lane],file] + def meta_lane = (file.getName().contains('.lane')) ? (file =~ /\.lane(\d+)/)[0][1].toInteger() : null //extracts number after ".lane" until next "_", must be int to match lane value from meta + [ [id: meta_id, lane: meta_lane], file ] } ch_samplesheet_new = ch_samplesheet .join( ch_samplesheet_no_adapter, failOnMismatch: true ) - .map{ meta,samplesheet,flowcell,lane,new_samplesheet -> [meta,new_samplesheet,flowcell,lane] } + .map{ meta, samplesheet, flowcell, lane, new_samplesheet -> [meta, new_samplesheet, flowcell, lane] } ch_samplesheet = ch_samplesheet_new } else { ch_samplesheet @@ -93,7 +93,7 @@ workflow DEMULTIPLEX { // RUN samplesheet_validator samshee if (!("samshee" in skip_tools) && (params.demultiplexer in ["bcl2fastq", "bclconvert", "mkfastq"])){ SAMSHEE ( - ch_samplesheet.map{ meta, samplesheet, flowcell, lane -> [meta,samplesheet] }, + ch_samplesheet.map{ meta, samplesheet, flowcell, lane -> [ meta, samplesheet ] }, ch_validator_schema ) ch_versions = ch_versions.mix(SAMSHEE.out.versions) From c45c38fd4f892de4c7501e8102752bde4b5c542f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 19:11:13 +0200 Subject: [PATCH 27/37] update snapshots --- tests/bclconvert_mini.nf.test.snap | 338 +---------------------------- tests/kraken.nf.test | 2 +- tests/sgdemux.nf.test.snap | 2 - tests/skip_tools.nf.test.snap | 6 +- tests/test_pe.nf.test.snap | 4 +- 5 files changed, 7 insertions(+), 345 deletions(-) diff --git a/tests/bclconvert_mini.nf.test.snap b/tests/bclconvert_mini.nf.test.snap index 1964ed33..6e9e2b3e 100644 --- a/tests/bclconvert_mini.nf.test.snap +++ b/tests/bclconvert_mini.nf.test.snap @@ -1,356 +1,26 @@ { "BCL-CONVERT-mini": { "content": [ - 26, + 0, { - "BCLCONVERT": { - "bclconvert": "4.3.6" - }, - "FALCO": { - "falco": "1.2.1" - }, - "FASTP": { - "fastp": "0.23.4" - }, - "MD5SUM": { - "md5sum": 8.3 - }, "Workflow": { "nf-core/demultiplex": "v1.5.2" } }, [ - "fastq", - "fastq/HBRR1_S1_L001.samplesheet.csv", - "fastq/HBRR2_S2_L001.samplesheet.csv", - 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"fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,f8b94a819f2b15b5a47c4b1003c32a18", - "fastp_filtered_reads_plot.txt:md5,8ab004632691b04b665920977beb8924", - "fastqc-status-check-heatmap.txt:md5,d83c2ffc1881a8e9d519273cca0f3e7e", - "fastqc_adapter_content_plot.txt:md5,a209adf87470f3a106e95a8636199b66", - "fastqc_overrepresented_sequences_plot.txt:md5,bf4b46c609cb609742c369cb251f2e2c", - "fastqc_per_base_n_content_plot.txt:md5,b7793753c3e72a9ecf52e9be83024cb2", - "fastqc_per_base_sequence_quality_plot.txt:md5,d1c9f76c20c4940880126246fa2c3412", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,0b2a4ff7cf154b2a500236edd1e25702", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ee01bcc9619fbb1f817c6c892743f25f", - "fastqc_per_sequence_quality_scores_plot.txt:md5,97c62777c755c89ed8e7ca802a111329", - "fastqc_sequence_counts_plot.txt:md5,4b906147cf7e362c83df2bf639d9c213", - "fastqc_sequence_duplication_levels_plot.txt:md5,6da1431aca488bb451e8a2b03dcb1d59", - "fastqc_sequence_length_distribution_plot.txt:md5,70de269b5d06021f286c44d3ac91b54b", - "fastqc_top_overrepresented_sequences_table.txt:md5,f222de753e55d387cc3a20f47520e60d", - "multiqc_bclconvert_bylane.txt:md5,5067dc968fcca1f47db0663f4d407807", - "multiqc_bclconvert_bysample.txt:md5,29634775947e43972c864bdb08ceb61e", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_general_stats.txt:md5,deb3d4f0bd64562ee425ddd34705e832" + "miniseq_truseq_smrna_no_adapters.csv:md5,c32433167a5c56d5c15952c2e7948898" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T16:52:45.476759" + "timestamp": "2024-10-15T18:46:20.011026" } } \ No newline at end of file diff --git a/tests/kraken.nf.test b/tests/kraken.nf.test index 3f050e9d..ec4cead7 100644 --- a/tests/kraken.nf.test +++ b/tests/kraken.nf.test @@ -2,7 +2,7 @@ nextflow_pipeline { name "Test Workflow main.nf - Kraken" script "../main.nf" - config "../../conf/test_kraken.config" + config "../conf/test_kraken.config" profile "test" tag "kraken" tag "pipeline" diff --git a/tests/sgdemux.nf.test.snap b/tests/sgdemux.nf.test.snap index 711cf84f..bd543246 100644 --- a/tests/sgdemux.nf.test.snap +++ b/tests/sgdemux.nf.test.snap @@ -546,8 +546,6 @@ "fastqc-2_sequence_duplication_levels_plot.txt:md5,a524a5e16ed509a3615ea05aa6d36bd0", "fastqc-2_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_fastqc.txt:md5,a7c0f80472810bed081063e213e4f972", - "multiqc_fastqc_1.txt:md5,841b89f28d4c48114a6bd02095f82bc8", "multiqc_general_stats.txt:md5,a8e26d200183fc9d9adb36e6a4a8dc27", "sim-data.csv:md5,a5ea0ad63c5df73b5fc2436dd8d9dbfe", "Undetermined_S25_L001.fastp.json:md5,577922aa75bb6ab549ed7699ae45becc", diff --git a/tests/skip_tools.nf.test.snap b/tests/skip_tools.nf.test.snap index 94936415..854a44d4 100644 --- a/tests/skip_tools.nf.test.snap +++ b/tests/skip_tools.nf.test.snap @@ -184,7 +184,6 @@ "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "multiqc_fastqc.txt:md5,a894d852b250ee902d805b358c173b88", "multiqc_general_stats.txt:md5,9e6cd051b09056263f269029b21a643b" ] ], @@ -424,7 +423,6 @@ "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_fastqc.txt:md5,a894d852b250ee902d805b358c173b88", "multiqc_general_stats.txt:md5,365ea22923184f063b3ad7bd75d7d910" ] ], @@ -716,7 +714,6 @@ "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "multiqc_fastqc.txt:md5,a894d852b250ee902d805b358c173b88", "multiqc_general_stats.txt:md5,9e6cd051b09056263f269029b21a643b" ] ], @@ -958,7 +955,6 @@ "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_fastqc.txt:md5,340a4f3f2e805633ca3490d0297be938", "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" ] ], @@ -968,4 +964,4 @@ }, "timestamp": "2024-10-15T14:38:35.728344" } -} \ No newline at end of file +} diff --git a/tests/test_pe.nf.test.snap b/tests/test_pe.nf.test.snap index dea1698d..8dcfc7f9 100644 --- a/tests/test_pe.nf.test.snap +++ b/tests/test_pe.nf.test.snap @@ -318,8 +318,6 @@ "fastqc-2_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "multiqc_bcl2fastq_bysample.txt:md5,bc5b6bbdcd75ead5a552cef09fc9aaec", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_fastqc.txt:md5,c92c8b128147b853b6820ca1025a388c", - "multiqc_fastqc_1.txt:md5,5445b6836eaa111b5d4b73bc126afe38", "multiqc_general_stats.txt:md5,2b3479c83a80205dca8db22279aac0fe" ] ], @@ -329,4 +327,4 @@ }, "timestamp": "2024-10-15T14:42:45.369275" } -} \ No newline at end of file +} From c60245cbc06717021d4f2891862fbd75e4352b54 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 16 Oct 2024 11:02:21 +0200 Subject: [PATCH 28/37] fix bclconvert_mini --- assets/schema_input.json | 1 + tests/bclconvert_mini.nf.test.snap | 338 ++++++++++++++++++++++++++++- 2 files changed, 335 insertions(+), 4 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index d4ce8dd4..9c8ae453 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -25,6 +25,7 @@ "type": "integer", "description": "Lane number", "minimum": 1, + "default": null, "maximum": 8, "meta": ["lane"] }, diff --git a/tests/bclconvert_mini.nf.test.snap b/tests/bclconvert_mini.nf.test.snap index 6e9e2b3e..49e6497f 100644 --- a/tests/bclconvert_mini.nf.test.snap +++ b/tests/bclconvert_mini.nf.test.snap @@ -1,26 +1,356 @@ { "BCL-CONVERT-mini": { "content": [ - 0, + 26, { + "BCLCONVERT": { + "bclconvert": "4.3.6" + }, + "FALCO": { + "falco": "1.2.1" + }, + "FASTP": { + "fastp": "0.23.4" + }, + "MD5SUM": { + "md5sum": 8.3 + }, "Workflow": { "nf-core/demultiplex": "v1.5.2" } }, [ + "fastq", + "fastq/HBRR1_S1_L001.samplesheet.csv", + "fastq/HBRR2_S2_L001.samplesheet.csv", + "fastq/HBRR3_S3_L001.samplesheet.csv", + "fastq/UHRR1_S4_L001.samplesheet.csv", + "fastq/UHRR2_S5_L001.samplesheet.csv", + "fastq/UHRR3_S6_L001.samplesheet.csv", + "miniseq_truseq_smrna", + "miniseq_truseq_smrna/HBRR1_S1_L001.fastp.fastq.gz", + "miniseq_truseq_smrna/HBRR1_S1_L001.fastp.fastq.gz.md5", + "miniseq_truseq_smrna/HBRR1_S1_L001.fastp.html", + "miniseq_truseq_smrna/HBRR1_S1_L001.fastp.json", + "miniseq_truseq_smrna/HBRR1_S1_L001_R1_001.fastq.gz", + "miniseq_truseq_smrna/HBRR1_S1_L001_fastqc_data.txt", + "miniseq_truseq_smrna/HBRR1_S1_L001_report.html", + "miniseq_truseq_smrna/HBRR1_S1_L001_summary.txt", + "miniseq_truseq_smrna/HBRR2_S2_L001.fastp.fastq.gz", + "miniseq_truseq_smrna/HBRR2_S2_L001.fastp.fastq.gz.md5", + "miniseq_truseq_smrna/HBRR2_S2_L001.fastp.html", + "miniseq_truseq_smrna/HBRR2_S2_L001.fastp.json", + "miniseq_truseq_smrna/HBRR2_S2_L001_R1_001.fastq.gz", + "miniseq_truseq_smrna/HBRR2_S2_L001_fastqc_data.txt", + "miniseq_truseq_smrna/HBRR2_S2_L001_report.html", + "miniseq_truseq_smrna/HBRR2_S2_L001_summary.txt", + "miniseq_truseq_smrna/HBRR3_S3_L001.fastp.fastq.gz", + "miniseq_truseq_smrna/HBRR3_S3_L001.fastp.fastq.gz.md5", + "miniseq_truseq_smrna/HBRR3_S3_L001.fastp.html", + "miniseq_truseq_smrna/HBRR3_S3_L001.fastp.json", + "miniseq_truseq_smrna/HBRR3_S3_L001_R1_001.fastq.gz", + "miniseq_truseq_smrna/HBRR3_S3_L001_fastqc_data.txt", + "miniseq_truseq_smrna/HBRR3_S3_L001_report.html", + "miniseq_truseq_smrna/HBRR3_S3_L001_summary.txt", + "miniseq_truseq_smrna/InterOp", 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"2024-10-16T10:59:08.175426" } } \ No newline at end of file From 5b20a6dc812eba8b29775a3bb463d6d6c6eec77e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 16 Oct 2024 11:13:22 +0200 Subject: [PATCH 29/37] update .nftignore and snapshots --- tests/.nftignore | 1 + tests/bcl2fastq.nf.test.snap | 3 +-- tests/bclconvert.nf.test.snap | 3 +-- tests/bclconvert_mini.nf.test.snap | 3 +-- tests/kraken.nf.test.snap | 3 +-- tests/skip_tools.nf.test.snap | 4 ---- 6 files changed, 5 insertions(+), 12 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 6453b710..31a3c488 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -7,6 +7,7 @@ **/Stats/Stats.json fastq/*.samplesheet.csv multiqc/multiqc_data/bcl2fastq_undetermined.txt +multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt multiqc/multiqc_data/multiqc.log multiqc/multiqc_data/multiqc_bcl2fastq_bylane.txt multiqc/multiqc_data/multiqc_data.json diff --git a/tests/bcl2fastq.nf.test.snap b/tests/bcl2fastq.nf.test.snap index a52d8832..216a38e6 100644 --- a/tests/bcl2fastq.nf.test.snap +++ b/tests/bcl2fastq.nf.test.snap @@ -232,7 +232,6 @@ "fastqc_per_sequence_quality_scores_plot.txt:md5,edbe64e0545cb866af73a649349d2a42", "fastqc_sequence_counts_plot.txt:md5,662c69090978601ca7d39504b1ac736b", "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", - "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "multiqc_bcl2fastq_bysample.txt:md5,baaa56d8315c18633f6ce6568d6f0657", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", "multiqc_general_stats.txt:md5,9aed65a87e63b8c0c5f7ef639eea81f3" @@ -244,4 +243,4 @@ }, "timestamp": "2024-10-15T16:39:25.304794" } -} \ No newline at end of file +} diff --git a/tests/bclconvert.nf.test.snap b/tests/bclconvert.nf.test.snap index 3145a5ac..4331e27d 100644 --- a/tests/bclconvert.nf.test.snap +++ b/tests/bclconvert.nf.test.snap @@ -227,7 +227,6 @@ "fastqc_per_sequence_quality_scores_plot.txt:md5,edbe64e0545cb866af73a649349d2a42", "fastqc_sequence_counts_plot.txt:md5,662c69090978601ca7d39504b1ac736b", "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", - "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", @@ -240,4 +239,4 @@ }, "timestamp": "2024-10-15T16:41:01.01928" } -} \ No newline at end of file +} diff --git a/tests/bclconvert_mini.nf.test.snap b/tests/bclconvert_mini.nf.test.snap index 49e6497f..8941ad94 100644 --- a/tests/bclconvert_mini.nf.test.snap +++ b/tests/bclconvert_mini.nf.test.snap @@ -340,7 +340,6 @@ "fastqc_sequence_counts_plot.txt:md5,4b906147cf7e362c83df2bf639d9c213", "fastqc_sequence_duplication_levels_plot.txt:md5,6da1431aca488bb451e8a2b03dcb1d59", "fastqc_sequence_length_distribution_plot.txt:md5,70de269b5d06021f286c44d3ac91b54b", - "fastqc_top_overrepresented_sequences_table.txt:md5,e38e7acf07858211dd44a8dddaec16a7", "multiqc_bclconvert_bylane.txt:md5,5067dc968fcca1f47db0663f4d407807", "multiqc_bclconvert_bysample.txt:md5,29634775947e43972c864bdb08ceb61e", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", @@ -353,4 +352,4 @@ }, "timestamp": "2024-10-16T10:59:08.175426" } -} \ No newline at end of file +} diff --git a/tests/kraken.nf.test.snap b/tests/kraken.nf.test.snap index 8d1fa326..4ce47ef9 100644 --- a/tests/kraken.nf.test.snap +++ b/tests/kraken.nf.test.snap @@ -248,7 +248,6 @@ "fastqc_per_sequence_quality_scores_plot.txt:md5,edbe64e0545cb866af73a649349d2a42", "fastqc_sequence_counts_plot.txt:md5,662c69090978601ca7d39504b1ac736b", "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", - "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "kraken-top-n-plot.txt:md5,add0b89a8b3d1729dac311870959b1e7", "multiqc_bcl2fastq_bysample.txt:md5,baaa56d8315c18633f6ce6568d6f0657", "multiqc_citations.txt:md5,97f1dcb4348072ce2865c29c5c306a3d", @@ -262,4 +261,4 @@ }, "timestamp": "2024-10-15T16:57:22.70902" } -} \ No newline at end of file +} diff --git a/tests/skip_tools.nf.test.snap b/tests/skip_tools.nf.test.snap index 854a44d4..89298dc7 100644 --- a/tests/skip_tools.nf.test.snap +++ b/tests/skip_tools.nf.test.snap @@ -180,7 +180,6 @@ "fastqc_per_sequence_quality_scores_plot.txt:md5,4bddb539b536979f004777303a749f06", "fastqc_sequence_counts_plot.txt:md5,32328f3e3421124466497ebebf458450", "fastqc_sequence_duplication_levels_plot.txt:md5,a3bf17370e71c501f610c5fc6b2ec292", - "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", @@ -419,7 +418,6 @@ "fastqc_per_sequence_quality_scores_plot.txt:md5,4bddb539b536979f004777303a749f06", "fastqc_sequence_counts_plot.txt:md5,32328f3e3421124466497ebebf458450", "fastqc_sequence_duplication_levels_plot.txt:md5,a3bf17370e71c501f610c5fc6b2ec292", - "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", @@ -710,7 +708,6 @@ "fastqc_per_sequence_quality_scores_plot.txt:md5,4bddb539b536979f004777303a749f06", "fastqc_sequence_counts_plot.txt:md5,32328f3e3421124466497ebebf458450", "fastqc_sequence_duplication_levels_plot.txt:md5,a3bf17370e71c501f610c5fc6b2ec292", - "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", @@ -951,7 +948,6 @@ "fastqc_per_sequence_quality_scores_plot.txt:md5,edbe64e0545cb866af73a649349d2a42", "fastqc_sequence_counts_plot.txt:md5,662c69090978601ca7d39504b1ac736b", "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", - "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", From e75b8ce7e22ecb1473995b4d0d8c7b90dd34ffb5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 16 Oct 2024 11:29:38 +0200 Subject: [PATCH 30/37] update .nftignore and snapshots --- tests/.nftignore | 5 + tests/bcl2fastq.nf.test.snap | 3 +- tests/bclconvert.nf.test.snap | 3 +- tests/bclconvert_mini.nf.test.snap | 3 +- tests/kraken.nf.test.snap | 1 - tests/mkfastq.nf.test.snap | 5 +- tests/sgdemux.nf.test.snap | 203 ----------------------------- tests/skip_tools.nf.test.snap | 3 +- tests/test_pe.nf.test.snap | 3 +- 9 files changed, 12 insertions(+), 217 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 31a3c488..0ce625e4 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -7,6 +7,7 @@ **/Stats/Stats.json fastq/*.samplesheet.csv multiqc/multiqc_data/bcl2fastq_undetermined.txt +multiqc/multiqc_data/fastqc-*-status-check-heatmap.txt multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt multiqc/multiqc_data/multiqc.log multiqc/multiqc_data/multiqc_bcl2fastq_bylane.txt @@ -14,6 +15,7 @@ multiqc/multiqc_data/multiqc_data.json multiqc/multiqc_data/multiqc_fastp.txt multiqc/multiqc_data/multiqc_fastqc.txt multiqc/multiqc_data/multiqc_fastqc_*.txt +multiqc/multiqc_data/multiqc_general_stats.txt multiqc/multiqc_data/multiqc_software_versions.txt multiqc/multiqc_data/multiqc_sources.txt multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} @@ -22,4 +24,7 @@ pipeline_info/*.{html,json,txt,yml} samplesheet/samplesheet.csv sim-data/*.fastp.fastq.gz sim-data/*.fastp.fastq.gz.md5 +sim-data/*.fastp.fastq.gz_fastqc_data.txt +sim-data/*.fastp.fastq.gz_fastqc_report.html +sim-data/*.fastp.fastq.gz_summary.txt sim-data/most_frequent_unmatched.tsv diff --git a/tests/bcl2fastq.nf.test.snap b/tests/bcl2fastq.nf.test.snap index 216a38e6..7f013b24 100644 --- a/tests/bcl2fastq.nf.test.snap +++ b/tests/bcl2fastq.nf.test.snap @@ -233,8 +233,7 @@ "fastqc_sequence_counts_plot.txt:md5,662c69090978601ca7d39504b1ac736b", "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", "multiqc_bcl2fastq_bysample.txt:md5,baaa56d8315c18633f6ce6568d6f0657", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_general_stats.txt:md5,9aed65a87e63b8c0c5f7ef639eea81f3" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" ] ], "meta": { diff --git a/tests/bclconvert.nf.test.snap b/tests/bclconvert.nf.test.snap index 4331e27d..b7d2c6b1 100644 --- a/tests/bclconvert.nf.test.snap +++ b/tests/bclconvert.nf.test.snap @@ -229,8 +229,7 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" ] ], "meta": { diff --git a/tests/bclconvert_mini.nf.test.snap b/tests/bclconvert_mini.nf.test.snap index 8941ad94..da1868bb 100644 --- a/tests/bclconvert_mini.nf.test.snap +++ b/tests/bclconvert_mini.nf.test.snap @@ -342,8 +342,7 @@ "fastqc_sequence_length_distribution_plot.txt:md5,70de269b5d06021f286c44d3ac91b54b", "multiqc_bclconvert_bylane.txt:md5,5067dc968fcca1f47db0663f4d407807", "multiqc_bclconvert_bysample.txt:md5,29634775947e43972c864bdb08ceb61e", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_general_stats.txt:md5,deb3d4f0bd64562ee425ddd34705e832" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" ] ], "meta": { diff --git a/tests/kraken.nf.test.snap b/tests/kraken.nf.test.snap index 4ce47ef9..f9126ef1 100644 --- a/tests/kraken.nf.test.snap +++ b/tests/kraken.nf.test.snap @@ -251,7 +251,6 @@ "kraken-top-n-plot.txt:md5,add0b89a8b3d1729dac311870959b1e7", "multiqc_bcl2fastq_bysample.txt:md5,baaa56d8315c18633f6ce6568d6f0657", "multiqc_citations.txt:md5,97f1dcb4348072ce2865c29c5c306a3d", - "multiqc_general_stats.txt:md5,2b86df713f6998ec0468bc4c9a6ec7a3", "multiqc_kraken.txt:md5,a90fd69786a0df1e43b948e423545654" ] ], diff --git a/tests/mkfastq.nf.test.snap b/tests/mkfastq.nf.test.snap index 30878dec..1e069fbf 100644 --- a/tests/mkfastq.nf.test.snap +++ b/tests/mkfastq.nf.test.snap @@ -209,8 +209,7 @@ "fastp-seq-quality-plot_Read_2_After_filtering.txt:md5,d6fc359d4e2be31d802b8553bcf5af93", "fastp-seq-quality-plot_Read_2_Before_filtering.txt:md5,e80f62d45ca21cacbd19f899f768c308", "fastp_filtered_reads_plot.txt:md5,39d2e637c3e1482821c62c00482c8421", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_general_stats.txt:md5,94b2ad1b21c8f69fd2b57102d52aa7c2" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" ] ], "meta": { @@ -219,4 +218,4 @@ }, "timestamp": "2024-10-15T14:34:23.682439" } -} \ No newline at end of file +} diff --git a/tests/sgdemux.nf.test.snap b/tests/sgdemux.nf.test.snap index bd543246..5726d115 100644 --- a/tests/sgdemux.nf.test.snap +++ b/tests/sgdemux.nf.test.snap @@ -527,7 +527,6 @@ "fastp-seq-quality-plot_Read_2_After_filtering.txt:md5,b5e3d7a8aca6895859654a4115b38708", "fastp-seq-quality-plot_Read_2_Before_filtering.txt:md5,b5e3d7a8aca6895859654a4115b38708", "fastp_filtered_reads_plot.txt:md5,0e60fe7db5d84497e03d814a9818e4c4", - "fastqc-1-status-check-heatmap.txt:md5,5703a024d73268bec3d4e6c74eae0015", "fastqc-1_per_base_n_content_plot.txt:md5,c0d889e3447bb580a91c26d58367ea3d", "fastqc-1_per_base_sequence_quality_plot.txt:md5,fc98fee907d0942dc1e0a2c046e697fc", "fastqc-1_per_sequence_gc_content_plot_Counts.txt:md5,d76e3dbdcdcbb0c5dc60912c275be5e1", @@ -536,7 +535,6 @@ "fastqc-1_sequence_counts_plot.txt:md5,020f9eacc4ddf1eef1f4187a3cf0122e", "fastqc-1_sequence_duplication_levels_plot.txt:md5,3c42607c5bda6eb3d39f45982f1c8e53", "fastqc-1_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "fastqc-2-status-check-heatmap.txt:md5,b8be3788e4b8cee928fd5b5314741ead", "fastqc-2_per_base_n_content_plot.txt:md5,dee7d9c094c60dc3a67c4da1954303f2", "fastqc-2_per_base_sequence_quality_plot.txt:md5,5d63f6647b7589d04bf2f2f9db88f584", "fastqc-2_per_sequence_gc_content_plot_Counts.txt:md5,ae1a7e984622d704f03cb658d5f160f5", @@ -546,237 +544,36 @@ "fastqc-2_sequence_duplication_levels_plot.txt:md5,a524a5e16ed509a3615ea05aa6d36bd0", "fastqc-2_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_general_stats.txt:md5,a8e26d200183fc9d9adb36e6a4a8dc27", "sim-data.csv:md5,a5ea0ad63c5df73b5fc2436dd8d9dbfe", "Undetermined_S25_L001.fastp.json:md5,577922aa75bb6ab549ed7699ae45becc", - "Undetermined_S25_L001_1.fastp.fastq.gz:md5,0b47650d469e68b468216d386e2af694", - "Undetermined_S25_L001_1.fastp.fastq.gz.md5:md5,3684fe515dc0d5647eab81f7131b3d2c", - "Undetermined_S25_L001_1.fastp.fastq.gz_fastqc_data.txt:md5,acd4d562ffe24343eabfd82b7d0f6b8c", - "Undetermined_S25_L001_1.fastp.fastq.gz_summary.txt:md5,2773a074bb5a71968f1dd98118ae4e76", - 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"sample_barcode_hop_metrics.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], diff --git a/tests/skip_tools.nf.test.snap b/tests/skip_tools.nf.test.snap index 89298dc7..45bd5938 100644 --- a/tests/skip_tools.nf.test.snap +++ b/tests/skip_tools.nf.test.snap @@ -182,8 +182,7 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,a3bf17370e71c501f610c5fc6b2ec292", "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "multiqc_general_stats.txt:md5,9e6cd051b09056263f269029b21a643b" + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], "meta": { diff --git a/tests/test_pe.nf.test.snap b/tests/test_pe.nf.test.snap index 8dcfc7f9..5301d971 100644 --- a/tests/test_pe.nf.test.snap +++ b/tests/test_pe.nf.test.snap @@ -317,8 +317,7 @@ "fastqc-2_sequence_duplication_levels_plot.txt:md5,02c6dcf1a65b7b3a21d8deaf70c8f3ca", "fastqc-2_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "multiqc_bcl2fastq_bysample.txt:md5,bc5b6bbdcd75ead5a552cef09fc9aaec", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_general_stats.txt:md5,2b3479c83a80205dca8db22279aac0fe" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" ] ], "meta": { From cda34234b2a4d0955ea7e15d04d8f74d6ed0b53d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 16 Oct 2024 11:37:09 +0200 Subject: [PATCH 31/37] update snapshots --- tests/skip_tools.nf.test.snap | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/tests/skip_tools.nf.test.snap b/tests/skip_tools.nf.test.snap index 45bd5938..2526e74c 100644 --- a/tests/skip_tools.nf.test.snap +++ b/tests/skip_tools.nf.test.snap @@ -419,8 +419,7 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,a3bf17370e71c501f610c5fc6b2ec292", "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_general_stats.txt:md5,365ea22923184f063b3ad7bd75d7d910" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" ] ], "meta": { @@ -709,8 +708,7 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,a3bf17370e71c501f610c5fc6b2ec292", "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "multiqc_general_stats.txt:md5,9e6cd051b09056263f269029b21a643b" + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], "meta": { @@ -949,8 +947,7 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "multiqc_general_stats.txt:md5,d2da854f7adc41c86d91b30ff0d758c4" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" ] ], "meta": { From 341974bec31b14f675881a7826e43814774bb5b6 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 16 Oct 2024 13:28:00 +0200 Subject: [PATCH 32/37] update .nftignore and snapshots --- tests/.nftignore | 2 +- tests/bases2fastq.nf.test.snap | 203 ++++++++++++++++++++++++++++- tests/bcl2fastq.nf.test.snap | 1 - tests/bclconvert.nf.test.snap | 1 - tests/bclconvert_mini.nf.test.snap | 1 - tests/kraken.nf.test.snap | 1 - tests/sgdemux.nf.test.snap | 1 - tests/skip_tools.nf.test.snap | 4 - tests/test_pe.nf.test.snap | 2 - 9 files changed, 200 insertions(+), 16 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 0ce625e4..d0ed2008 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -7,7 +7,7 @@ **/Stats/Stats.json fastq/*.samplesheet.csv multiqc/multiqc_data/bcl2fastq_undetermined.txt -multiqc/multiqc_data/fastqc-*-status-check-heatmap.txt +multiqc/multiqc_data/fastqc*status-check-heatmap.txt multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt multiqc/multiqc_data/multiqc.log multiqc/multiqc_data/multiqc_bcl2fastq_bylane.txt diff --git a/tests/bases2fastq.nf.test.snap b/tests/bases2fastq.nf.test.snap index 52d3fbda..69a6c8b3 100644 --- a/tests/bases2fastq.nf.test.snap +++ b/tests/bases2fastq.nf.test.snap @@ -1,19 +1,214 @@ { "Bases2Fastq": { "content": [ - 0, + 8, { + "BASES2FASTQ": { + "bases2fastq": "1.8.0.1260801529, use subject to license available at elementbiosciences.com" + }, + "FALCO": { + "falco": "1.2.1" + }, + "FASTP": { + "fastp": "0.23.4" + }, + "MD5SUM": { + "md5sum": 8.3 + }, + "UNTAR_FLOWCELL": { + "untar": 1.34 + }, "Workflow": { "nf-core/demultiplex": "v1.5.2" } }, [ + "fastq", + "fastq/DefaultSample.samplesheet.csv", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/fastp-insert-size-plot.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_2_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_2_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_2_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_2_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_2_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_2_Before_filtering.txt", + "multiqc/multiqc_data/fastp_filtered_reads_plot.txt", + "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", + "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_fastp.txt", + "multiqc/multiqc_data/multiqc_fastqc.txt", + "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/fastp-insert-size-plot.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_2_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_2_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_1_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_1_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_2_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_2_Before_filtering.pdf", + 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+ "multiqc/multiqc_plots/svg/fastp-seq-content-n-plot_Read_1_Before_filtering.svg", + "multiqc/multiqc_plots/svg/fastp-seq-content-n-plot_Read_2_After_filtering.svg", + "multiqc/multiqc_plots/svg/fastp-seq-content-n-plot_Read_2_Before_filtering.svg", + "multiqc/multiqc_plots/svg/fastp-seq-quality-plot_Read_1_After_filtering.svg", + "multiqc/multiqc_plots/svg/fastp-seq-quality-plot_Read_1_Before_filtering.svg", + "multiqc/multiqc_plots/svg/fastp-seq-quality-plot_Read_2_After_filtering.svg", + "multiqc/multiqc_plots/svg/fastp-seq-quality-plot_Read_2_Before_filtering.svg", + "multiqc/multiqc_plots/svg/fastp_filtered_reads_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastp_filtered_reads_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_plots/svg/general_stats_table.svg", + "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", - "samplesheet" + "samplesheet", + "samplesheet/samplesheet.csv", + "sim-data", + "sim-data.csv", + "sim-data/20230404-Bases2Fastq-Sim_QC.html", + "sim-data/DefaultSample.fastp.html", + "sim-data/DefaultSample.fastp.json", + "sim-data/DefaultSample_1.fastp.fastq.gz", + "sim-data/DefaultSample_1.fastp.fastq.gz.md5", + "sim-data/DefaultSample_1.fastp.fastq.gz_fastqc_data.txt", + "sim-data/DefaultSample_1.fastp.fastq.gz_fastqc_report.html", + "sim-data/DefaultSample_1.fastp.fastq.gz_summary.txt", + "sim-data/DefaultSample_2.fastp.fastq.gz", + "sim-data/DefaultSample_2.fastp.fastq.gz.md5", + "sim-data/DefaultSample_2.fastp.fastq.gz_fastqc_data.txt", + "sim-data/DefaultSample_2.fastp.fastq.gz_fastqc_report.html", + "sim-data/DefaultSample_2.fastp.fastq.gz_summary.txt", + "sim-data/Metrics.csv", + "sim-data/RunManifest.json", + "sim-data/RunStats.json", + "sim-data/Samples", + "sim-data/Samples/DefaultProject", + "sim-data/Samples/DefaultProject/DefaultSample", + "sim-data/Samples/DefaultProject/DefaultSample/DefaultSample_R1.fastq.gz", + "sim-data/Samples/DefaultProject/DefaultSample/DefaultSample_R2.fastq.gz", + "sim-data/Samples/DefaultProject/DefaultSample/DefaultSample_stats.json", + "sim-data/UnassignedSequences.csv" ], [ - + "fastp-insert-size-plot.txt:md5,ac9a9c57ed6cbd69033968f727e755de", + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,fc7408bc90e9fd3768e041c470b297eb", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,f1b14d0b742540f46a447508b27c2a6d", + "fastp-seq-content-gc-plot_Read_2_After_filtering.txt:md5,df0d79b9296d4ee8996f2a28ccff4b65", + "fastp-seq-content-gc-plot_Read_2_Before_filtering.txt:md5,8f63cb5ddb7b4ebe8325271093018714", + "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,48fe699c2e7dfa81d9d97f53c613ef20", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,48fe699c2e7dfa81d9d97f53c613ef20", + "fastp-seq-content-n-plot_Read_2_After_filtering.txt:md5,48fe699c2e7dfa81d9d97f53c613ef20", + "fastp-seq-content-n-plot_Read_2_Before_filtering.txt:md5,48fe699c2e7dfa81d9d97f53c613ef20", + "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,e2194a8841653929cad0847f64daa339", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,559b29beffa82c35c71a82c3ff459a40", + "fastp-seq-quality-plot_Read_2_After_filtering.txt:md5,62a344d18de885a880e8a9fe48c7816f", + "fastp-seq-quality-plot_Read_2_Before_filtering.txt:md5,5ef421e1df317a359c8b27ff65f2b758", + "fastp_filtered_reads_plot.txt:md5,5a5a98b82c02875b4d9da92e7577e802", + "fastqc_per_base_n_content_plot.txt:md5,7a1a9b3df3ce3bcca265dd13f2e23dc0", + "fastqc_per_base_sequence_quality_plot.txt:md5,9f62301e59b368cdd6738cbd871a964e", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ebee4de078cbb125ba741a21d3552900", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,58b7050c7f02baa7fc308c691e62cc4c", + "fastqc_per_sequence_quality_scores_plot.txt:md5,dd7520f2fd44bfb2fa67f8ff9f7237a5", + "fastqc_sequence_counts_plot.txt:md5,e8772d59c78943686597222939492e1e", + "fastqc_sequence_duplication_levels_plot.txt:md5,4b372fcce4dbb8b0dbe685c6380f4a97", + "fastqc_sequence_length_distribution_plot.txt:md5,5b002b51364b518093ad98ebe0a0ca39", + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", + "sim-data.csv:md5,1d1dab697bd88c411fff89c102024295", + "20230404-Bases2Fastq-Sim_QC.html:md5,cad670fb51b11bd922fb043a3cd20933", + "DefaultSample.fastp.json:md5,9c10bbfbc4beb9523ca3a114f95709db", + "Metrics.csv:md5,ad7af77573845924062e2554cc641b16", + "RunManifest.json:md5,cdb8051690645d0f070191286323f1c8", + "RunStats.json:md5,052d3c470e14f5ffe7c3d95fa89fc91d", + "DefaultSample_R1.fastq.gz:md5,6c73b924e4eb53b716614aa6fd8b791a", + "DefaultSample_R2.fastq.gz:md5,54e2c0894844e42605b7cd567b1c7dbe", + "DefaultSample_stats.json:md5,950f61efbca180df8e5cf519ff05ada2", + "UnassignedSequences.csv:md5,11c1693830ce941b8cfb8d2431a59097" ] ], "meta": { @@ -22,4 +217,4 @@ }, "timestamp": "2024-10-15T16:37:55.855747" } -} \ No newline at end of file +} diff --git a/tests/bcl2fastq.nf.test.snap b/tests/bcl2fastq.nf.test.snap index 7f013b24..7fb8ea17 100644 --- a/tests/bcl2fastq.nf.test.snap +++ b/tests/bcl2fastq.nf.test.snap @@ -224,7 +224,6 @@ "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,1701b40c23dca068210f5410788e3be1", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,35de9aebdc467b1bbc9fd1f40d3aece4", "fastp_filtered_reads_plot.txt:md5,fa14a1941e109d4104c33db0e5fe20fc", - "fastqc-status-check-heatmap.txt:md5,ba346b48736a57f50aa1ef5ce468f5df", "fastqc_per_base_n_content_plot.txt:md5,d7db99124db8f53d82c51c779ce77463", "fastqc_per_base_sequence_quality_plot.txt:md5,31c51bbd7d4dbb32107efa95c8a58ee5", "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,842eaa1c62a8e6676b4b07226bda998b", diff --git a/tests/bclconvert.nf.test.snap b/tests/bclconvert.nf.test.snap index b7d2c6b1..f064c458 100644 --- a/tests/bclconvert.nf.test.snap +++ b/tests/bclconvert.nf.test.snap @@ -219,7 +219,6 @@ "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,1701b40c23dca068210f5410788e3be1", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,35de9aebdc467b1bbc9fd1f40d3aece4", "fastp_filtered_reads_plot.txt:md5,fa14a1941e109d4104c33db0e5fe20fc", - "fastqc-status-check-heatmap.txt:md5,ba346b48736a57f50aa1ef5ce468f5df", "fastqc_per_base_n_content_plot.txt:md5,d7db99124db8f53d82c51c779ce77463", "fastqc_per_base_sequence_quality_plot.txt:md5,31c51bbd7d4dbb32107efa95c8a58ee5", "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,842eaa1c62a8e6676b4b07226bda998b", diff --git a/tests/bclconvert_mini.nf.test.snap b/tests/bclconvert_mini.nf.test.snap index da1868bb..77ba8a65 100644 --- a/tests/bclconvert_mini.nf.test.snap +++ b/tests/bclconvert_mini.nf.test.snap @@ -329,7 +329,6 @@ "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,d1c9f76c20c4940880126246fa2c3412", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,f8b94a819f2b15b5a47c4b1003c32a18", "fastp_filtered_reads_plot.txt:md5,8ab004632691b04b665920977beb8924", - "fastqc-status-check-heatmap.txt:md5,d83c2ffc1881a8e9d519273cca0f3e7e", "fastqc_adapter_content_plot.txt:md5,a209adf87470f3a106e95a8636199b66", "fastqc_overrepresented_sequences_plot.txt:md5,bf4b46c609cb609742c369cb251f2e2c", "fastqc_per_base_n_content_plot.txt:md5,b7793753c3e72a9ecf52e9be83024cb2", diff --git a/tests/kraken.nf.test.snap b/tests/kraken.nf.test.snap index f9126ef1..36a6b165 100644 --- a/tests/kraken.nf.test.snap +++ b/tests/kraken.nf.test.snap @@ -240,7 +240,6 @@ "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,1701b40c23dca068210f5410788e3be1", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,35de9aebdc467b1bbc9fd1f40d3aece4", "fastp_filtered_reads_plot.txt:md5,fa14a1941e109d4104c33db0e5fe20fc", - "fastqc-status-check-heatmap.txt:md5,ba346b48736a57f50aa1ef5ce468f5df", "fastqc_per_base_n_content_plot.txt:md5,d7db99124db8f53d82c51c779ce77463", "fastqc_per_base_sequence_quality_plot.txt:md5,31c51bbd7d4dbb32107efa95c8a58ee5", "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,842eaa1c62a8e6676b4b07226bda998b", diff --git a/tests/sgdemux.nf.test.snap b/tests/sgdemux.nf.test.snap index 5726d115..e11ba9ee 100644 --- a/tests/sgdemux.nf.test.snap +++ b/tests/sgdemux.nf.test.snap @@ -547,7 +547,6 @@ "sim-data.csv:md5,a5ea0ad63c5df73b5fc2436dd8d9dbfe", "Undetermined_S25_L001.fastp.json:md5,577922aa75bb6ab549ed7699ae45becc", "metrics.tsv:md5,7627e4bd2a56ea551fd74b4a2b5cb4b2", - "most_frequent_unmatched.tsv:md5,89393e8796a9a6f86d0b3b1167677997", "per_project_metrics.tsv:md5,7393bc580c8ed8431107ad3dd00a7d2a", "per_sample_metrics.tsv:md5,fb8ce024ad2508e7b22a4af65fe44358", "s10_S10_L001.fastp.json:md5,80d48c6afeade19ad0d7abf001cd95c5", diff --git a/tests/skip_tools.nf.test.snap b/tests/skip_tools.nf.test.snap index 2526e74c..a7b0d626 100644 --- a/tests/skip_tools.nf.test.snap +++ b/tests/skip_tools.nf.test.snap @@ -172,7 +172,6 @@ "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", "bclconvert_sample_counts_Counts_per_lane.txt:md5,a7e57ab911ba2cf74ec7bd93b921036d", "bclconvert_sample_counts_Index_mismatches.txt:md5,06c29164e83815c79a2b1541a4a6294e", - "fastqc-status-check-heatmap.txt:md5,c0a0084f2fbd9d5aa410310ad1906002", "fastqc_per_base_n_content_plot.txt:md5,bc2bc3f88871a2fddf04d8b499fd4e70", "fastqc_per_base_sequence_quality_plot.txt:md5,0d82022063896dabc7ac5beb83a4bc54", "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,92e5327c241881220d4cd69b8fd29e4a", @@ -409,7 +408,6 @@ "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,1701b40c23dca068210f5410788e3be1", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,35de9aebdc467b1bbc9fd1f40d3aece4", "fastp_filtered_reads_plot.txt:md5,fa14a1941e109d4104c33db0e5fe20fc", - "fastqc-status-check-heatmap.txt:md5,c0a0084f2fbd9d5aa410310ad1906002", "fastqc_per_base_n_content_plot.txt:md5,bc2bc3f88871a2fddf04d8b499fd4e70", "fastqc_per_base_sequence_quality_plot.txt:md5,0d82022063896dabc7ac5beb83a4bc54", "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,92e5327c241881220d4cd69b8fd29e4a", @@ -698,7 +696,6 @@ "bclconvert_lane_counts.txt:md5,a327047d0d6c7de32eef9535bb159110", "bclconvert_sample_counts_Counts_per_lane.txt:md5,a7e57ab911ba2cf74ec7bd93b921036d", "bclconvert_sample_counts_Index_mismatches.txt:md5,06c29164e83815c79a2b1541a4a6294e", - "fastqc-status-check-heatmap.txt:md5,c0a0084f2fbd9d5aa410310ad1906002", "fastqc_per_base_n_content_plot.txt:md5,bc2bc3f88871a2fddf04d8b499fd4e70", "fastqc_per_base_sequence_quality_plot.txt:md5,0d82022063896dabc7ac5beb83a4bc54", "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,92e5327c241881220d4cd69b8fd29e4a", @@ -937,7 +934,6 @@ "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,1701b40c23dca068210f5410788e3be1", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,35de9aebdc467b1bbc9fd1f40d3aece4", "fastp_filtered_reads_plot.txt:md5,fa14a1941e109d4104c33db0e5fe20fc", - "fastqc-status-check-heatmap.txt:md5,ba346b48736a57f50aa1ef5ce468f5df", "fastqc_per_base_n_content_plot.txt:md5,d7db99124db8f53d82c51c779ce77463", "fastqc_per_base_sequence_quality_plot.txt:md5,31c51bbd7d4dbb32107efa95c8a58ee5", "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,842eaa1c62a8e6676b4b07226bda998b", diff --git a/tests/test_pe.nf.test.snap b/tests/test_pe.nf.test.snap index 5301d971..4e4248e6 100644 --- a/tests/test_pe.nf.test.snap +++ b/tests/test_pe.nf.test.snap @@ -298,7 +298,6 @@ "fastp-seq-quality-plot_Read_2_After_filtering.txt:md5,feb0492fc4a011f49b0ae771af00fad2", "fastp-seq-quality-plot_Read_2_Before_filtering.txt:md5,ced1654945cd8c6a85dbe3353959e4b1", "fastp_filtered_reads_plot.txt:md5,136a1d755ba6e790227f80cfcb4c1d62", - "fastqc-1-status-check-heatmap.txt:md5,4267503a162e5d5996f8e192272f3154", "fastqc-1_per_base_n_content_plot.txt:md5,2c2e1e7e982151328380d462bf3da96a", "fastqc-1_per_base_sequence_quality_plot.txt:md5,16c2db072409c63e9e72cc8b8efd7c1d", "fastqc-1_per_sequence_gc_content_plot_Counts.txt:md5,9e2aa8732545bf8544e03e8451d5d200", @@ -307,7 +306,6 @@ "fastqc-1_sequence_counts_plot.txt:md5,5ab45b6a9e87a73e919c9f27d686bf8d", "fastqc-1_sequence_duplication_levels_plot.txt:md5,47853398841fe7f3f8e2c930b8674247", "fastqc-1_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "fastqc-2-status-check-heatmap.txt:md5,91ec7ae5d40aa62546cee0608e65c10c", "fastqc-2_per_base_n_content_plot.txt:md5,ecb4ae5f410a79977f13f53743e61d88", "fastqc-2_per_base_sequence_quality_plot.txt:md5,dbefa9916514fc5161c358579fbf6abd", "fastqc-2_per_sequence_gc_content_plot_Counts.txt:md5,f1efe8f47e924cadd8a9f64b63b53d4d", From b8b6c9e05f5beb70c945c79f740b64f0a4c2a235 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 16 Oct 2024 13:48:32 +0200 Subject: [PATCH 33/37] update snapshots --- tests/fqtk.nf.test.snap | 718 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 714 insertions(+), 4 deletions(-) diff --git a/tests/fqtk.nf.test.snap b/tests/fqtk.nf.test.snap index f4d2401f..c5cbb5ec 100644 --- a/tests/fqtk.nf.test.snap +++ 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"unmatched_1.fastp.fastq.gz.md5:md5,5b5876132b859c7dc6558bc63b24f8bf", + "unmatched_1.fastp.fastq.gz_fastqc_data.txt:md5,03d2a927a8850e90f4401c5e7cb469ec", + "unmatched_1.fastp.fastq.gz_summary.txt:md5,8f82f5c293be99943424dd66ebc74627", + "unmatched_2.fastp.fastq.gz:md5,a2c623dcaa11fe3faaecc563c376f24b", + "unmatched_2.fastp.fastq.gz.md5:md5,ea51457970db5e6690a0f76cd2b6be85", + "unmatched_2.fastp.fastq.gz_fastqc_data.txt:md5,ba1ff6c0e111ebdb3a269a3add145ae6", + "unmatched_2.fastp.fastq.gz_summary.txt:md5,202c2d50118198e29ead032008eab7d6" ] ], "meta": { @@ -22,4 +732,4 @@ }, "timestamp": "2024-10-15T16:56:01.494868" } -} \ No newline at end of file +} From 6e5794ca8083a08f730586f15165a9d6224ce4d9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 16 Oct 2024 14:03:45 +0200 Subject: [PATCH 34/37] update .nftignore and snaps --- tests/.nftignore | 3 +++ tests/bases2fastq.nf.test.snap | 3 --- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index d0ed2008..b94ae7b4 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -22,9 +22,12 @@ multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html pipeline_info/*.{html,json,txt,yml} samplesheet/samplesheet.csv +sim-data/*-Bases2Fastq-Sim_QC.html sim-data/*.fastp.fastq.gz sim-data/*.fastp.fastq.gz.md5 sim-data/*.fastp.fastq.gz_fastqc_data.txt sim-data/*.fastp.fastq.gz_fastqc_report.html sim-data/*.fastp.fastq.gz_summary.txt +sim-data/RunStats.json +sim-data/Samples/DefaultProject/DefaultSample/DefaultSample_stats.json sim-data/most_frequent_unmatched.tsv diff --git a/tests/bases2fastq.nf.test.snap b/tests/bases2fastq.nf.test.snap index 69a6c8b3..317657ae 100644 --- a/tests/bases2fastq.nf.test.snap +++ b/tests/bases2fastq.nf.test.snap @@ -200,14 +200,11 @@ "fastqc_sequence_length_distribution_plot.txt:md5,5b002b51364b518093ad98ebe0a0ca39", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", "sim-data.csv:md5,1d1dab697bd88c411fff89c102024295", - "20230404-Bases2Fastq-Sim_QC.html:md5,cad670fb51b11bd922fb043a3cd20933", "DefaultSample.fastp.json:md5,9c10bbfbc4beb9523ca3a114f95709db", "Metrics.csv:md5,ad7af77573845924062e2554cc641b16", "RunManifest.json:md5,cdb8051690645d0f070191286323f1c8", - "RunStats.json:md5,052d3c470e14f5ffe7c3d95fa89fc91d", "DefaultSample_R1.fastq.gz:md5,6c73b924e4eb53b716614aa6fd8b791a", "DefaultSample_R2.fastq.gz:md5,54e2c0894844e42605b7cd567b1c7dbe", - "DefaultSample_stats.json:md5,950f61efbca180df8e5cf519ff05ada2", "UnassignedSequences.csv:md5,11c1693830ce941b8cfb8d2431a59097" ] ], From 594ef1f2b5d8996109bcfe297726edead29e2f5d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 16 Oct 2024 16:26:57 +0200 Subject: [PATCH 35/37] min time is 4h --- conf/test.config | 2 +- conf/test_bases2fastq.config | 2 +- conf/test_bcl2fastq.config | 2 +- conf/test_bclconvert.config | 2 +- conf/test_checkqc.config | 2 +- conf/test_fqtk.config | 2 +- conf/test_kraken.config | 2 +- conf/test_mkfastq.config | 2 +- conf/test_pe.config | 2 +- conf/test_sgdemux.config | 2 +- conf/test_two_lanes.config | 2 +- conf/test_uncompressed.config | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/conf/test.config b/conf/test.config index 1881ea37..639abb1d 100755 --- a/conf/test.config +++ b/conf/test.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '4.h' ] } diff --git a/conf/test_bases2fastq.config b/conf/test_bases2fastq.config index c852abf2..51f1dd52 100644 --- a/conf/test_bases2fastq.config +++ b/conf/test_bases2fastq.config @@ -15,7 +15,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '4.h' ] } diff --git a/conf/test_bcl2fastq.config b/conf/test_bcl2fastq.config index d8cec137..5caa08ad 100644 --- a/conf/test_bcl2fastq.config +++ b/conf/test_bcl2fastq.config @@ -15,7 +15,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '4.h' ] } diff --git a/conf/test_bclconvert.config b/conf/test_bclconvert.config index 0800e7ab..02de58cf 100755 --- a/conf/test_bclconvert.config +++ b/conf/test_bclconvert.config @@ -15,7 +15,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '4.h' ] } diff --git a/conf/test_checkqc.config b/conf/test_checkqc.config index 912fdf4b..c9af0454 100644 --- a/conf/test_checkqc.config +++ b/conf/test_checkqc.config @@ -15,7 +15,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '4.h' ] } diff --git a/conf/test_fqtk.config b/conf/test_fqtk.config index c09338f8..685132d6 100644 --- a/conf/test_fqtk.config +++ b/conf/test_fqtk.config @@ -15,7 +15,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '4.h' ] } diff --git a/conf/test_kraken.config b/conf/test_kraken.config index aaf650f3..746c9328 100644 --- a/conf/test_kraken.config +++ b/conf/test_kraken.config @@ -15,7 +15,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '4.h' ] } diff --git a/conf/test_mkfastq.config b/conf/test_mkfastq.config index 95a90039..0a3de8db 100644 --- a/conf/test_mkfastq.config +++ b/conf/test_mkfastq.config @@ -15,7 +15,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '4.h' ] } diff --git a/conf/test_pe.config b/conf/test_pe.config index 9cc44752..83bff290 100644 --- a/conf/test_pe.config +++ b/conf/test_pe.config @@ -15,7 +15,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '4.h' ] } diff --git a/conf/test_sgdemux.config b/conf/test_sgdemux.config index 0782451b..d1c1a3cb 100644 --- a/conf/test_sgdemux.config +++ b/conf/test_sgdemux.config @@ -15,7 +15,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '4.h' ] } diff --git a/conf/test_two_lanes.config b/conf/test_two_lanes.config index 42b91b7c..ee3cf53a 100644 --- a/conf/test_two_lanes.config +++ b/conf/test_two_lanes.config @@ -15,7 +15,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '4.h' ] } diff --git a/conf/test_uncompressed.config b/conf/test_uncompressed.config index da1a4dc6..0d0b2296 100644 --- a/conf/test_uncompressed.config +++ b/conf/test_uncompressed.config @@ -15,7 +15,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '4.h' ] } From 7211fe0bfb8a112bdf1cd4518f5e4b0a4dd81c4a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 17 Oct 2024 10:05:40 +0200 Subject: [PATCH 36/37] memory should be capped to 13.GB, not 15.GB --- conf/test.config | 2 +- conf/test_bases2fastq.config | 2 +- conf/test_bcl2fastq.config | 2 +- conf/test_bclconvert.config | 2 +- conf/test_checkqc.config | 2 +- conf/test_fqtk.config | 2 +- conf/test_kraken.config | 2 +- conf/test_mkfastq.config | 2 +- conf/test_pe.config | 2 +- conf/test_sgdemux.config | 2 +- conf/test_two_lanes.config | 2 +- conf/test_uncompressed.config | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/conf/test.config b/conf/test.config index 639abb1d..680c6cfd 100755 --- a/conf/test.config +++ b/conf/test.config @@ -13,7 +13,7 @@ process { resourceLimits = [ cpus: 4, - memory: '15.GB', + memory: '13.GB', time: '4.h' ] } diff --git a/conf/test_bases2fastq.config b/conf/test_bases2fastq.config index 51f1dd52..7b3764d8 100644 --- a/conf/test_bases2fastq.config +++ b/conf/test_bases2fastq.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, - memory: '15.GB', + memory: '13.GB', time: '4.h' ] } diff --git a/conf/test_bcl2fastq.config b/conf/test_bcl2fastq.config index 5caa08ad..d94b53e8 100644 --- a/conf/test_bcl2fastq.config +++ b/conf/test_bcl2fastq.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, - memory: '15.GB', + memory: '13.GB', time: '4.h' ] } diff --git a/conf/test_bclconvert.config b/conf/test_bclconvert.config index 02de58cf..2510ba6d 100755 --- a/conf/test_bclconvert.config +++ b/conf/test_bclconvert.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, - memory: '15.GB', + memory: '13.GB', time: '4.h' ] } diff --git a/conf/test_checkqc.config b/conf/test_checkqc.config index c9af0454..b6b971e0 100644 --- a/conf/test_checkqc.config +++ b/conf/test_checkqc.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, - memory: '15.GB', + memory: '13.GB', time: '4.h' ] } diff --git a/conf/test_fqtk.config b/conf/test_fqtk.config index 685132d6..ceac2c83 100644 --- a/conf/test_fqtk.config +++ b/conf/test_fqtk.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, - memory: '15.GB', + memory: '13.GB', time: '4.h' ] } diff --git a/conf/test_kraken.config b/conf/test_kraken.config index 746c9328..f4c0b609 100644 --- a/conf/test_kraken.config +++ b/conf/test_kraken.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, - memory: '15.GB', + memory: '13.GB', time: '4.h' ] } diff --git a/conf/test_mkfastq.config b/conf/test_mkfastq.config index 0a3de8db..070ebab5 100644 --- a/conf/test_mkfastq.config +++ b/conf/test_mkfastq.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, - memory: '15.GB', + memory: '13.GB', time: '4.h' ] } diff --git a/conf/test_pe.config b/conf/test_pe.config index 83bff290..cfcf0422 100644 --- a/conf/test_pe.config +++ b/conf/test_pe.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, - memory: '15.GB', + memory: '13.GB', time: '4.h' ] } diff --git a/conf/test_sgdemux.config b/conf/test_sgdemux.config index d1c1a3cb..db34a65b 100644 --- a/conf/test_sgdemux.config +++ b/conf/test_sgdemux.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, - memory: '15.GB', + memory: '13.GB', time: '4.h' ] } diff --git a/conf/test_two_lanes.config b/conf/test_two_lanes.config index ee3cf53a..d6f04923 100644 --- a/conf/test_two_lanes.config +++ b/conf/test_two_lanes.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, - memory: '15.GB', + memory: '13.GB', time: '4.h' ] } diff --git a/conf/test_uncompressed.config b/conf/test_uncompressed.config index 0d0b2296..a33378c2 100644 --- a/conf/test_uncompressed.config +++ b/conf/test_uncompressed.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, - memory: '15.GB', + memory: '13.GB', time: '4.h' ] } From 0408378e03f82e3bfab161e40428ff8df4fd67be Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 17 Oct 2024 10:50:24 +0200 Subject: [PATCH 37/37] update .nftignore and snapshots --- tests/.nftignore | 1 + tests/mkfastq.nf.test.snap | 14 -------------- 2 files changed, 1 insertion(+), 14 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index b94ae7b4..2c7e41e2 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -5,6 +5,7 @@ **/Stats/ConversionStats.xml **/Stats/DemuxSummaryF1L1.txt **/Stats/Stats.json +cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz fastq/*.samplesheet.csv multiqc/multiqc_data/bcl2fastq_undetermined.txt multiqc/multiqc_data/fastqc*status-check-heatmap.txt diff --git a/tests/mkfastq.nf.test.snap b/tests/mkfastq.nf.test.snap index 1e069fbf..c95a793e 100644 --- a/tests/mkfastq.nf.test.snap +++ b/tests/mkfastq.nf.test.snap @@ -174,20 +174,6 @@ "test_sample_S1_L001_1.fastp.fastq.gz.md5:md5,43d7882f3aaae47b56df56da6c802236", "test_sample_S1_L001_2.fastp.fastq.gz:md5,1c60f1f3958b8b2b0255b9fae6df0b3d", "test_sample_S1_L001_2.fastp.fastq.gz.md5:md5,01d742cc56639c476b0bac0c094eba4b", - { - "directory": false, - "file": true, - "freeSpace": 19969302528, - "canonicalPath": "/home/max/workspace/demultiplex/.nf-test/tests/ed2ff7c0bb8147747cb278f737effd34/output/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz", - "usableSpace": 7318863872, - "hidden": false, - "totalSpace": 247570337792, - "path": "/home/max/workspace/demultiplex/.nf-test/tests/ed2ff7c0bb8147747cb278f737effd34/output/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz", - "name": "test_sample_S1_L001_I1_001.fastp.fastq.gz", - "absolute": true, - "absolutePath": "/home/max/workspace/demultiplex/.nf-test/tests/ed2ff7c0bb8147747cb278f737effd34/output/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz", - "parent": "/home/max/workspace/demultiplex/.nf-test/tests/ed2ff7c0bb8147747cb278f737effd34/output/cellranger-tiny-bcl-simple/L001" - }, "test_sample_S1_L001_I1_001.fastp.fastq.gz.md5:md5,82e397b4a2418f27269a30f6ca0e349e", "test_sample_S1_L001_I1_001.fastp.json:md5,b5368b3125c35f7a5dfa2d273cd79c32", "test_sample_S1_L001_I1_001.fastq.gz:md5,018b0dbd8daf76fb9f6dfa4729ea0453",