From 63cb94d7391d3c7daade2e0387ddb63c62611c2e Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 8 May 2024 13:58:04 +0000 Subject: [PATCH 01/12] Template update for nf-core/tools version 2.14.0 --- .editorconfig | 6 +- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 10 +- .github/workflows/awstest.yml | 12 +- .github/workflows/ci.yml | 4 +- .github/workflows/download_pipeline.yml | 22 ++- .github/workflows/fix-linting.yml | 6 +- .github/workflows/linting.yml | 18 +- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 6 +- .nf-core.yml | 1 + .pre-commit-config.yaml | 3 + CHANGELOG.md | 2 +- README.md | 2 +- assets/multiqc_config.yml | 6 +- conf/base.config | 3 - conf/modules.config | 8 - conf/test.config | 2 +- conf/test_full.config | 2 +- docs/usage.md | 2 + modules.json | 4 +- modules/nf-core/fastqc/main.nf | 6 + nextflow.config | 178 +++++++++--------- nextflow_schema.json | 7 + pyproject.toml | 15 -- .../utils_nfcore_airrflow_pipeline/main.nf | 16 +- .../nf-core/utils_nfcore_pipeline/main.nf | 8 +- workflows/airrflow.nf | 46 +++-- 28 files changed, 226 insertions(+), 173 deletions(-) delete mode 100644 pyproject.toml diff --git a/.editorconfig b/.editorconfig index dd9ffa53..72dda289 100644 --- a/.editorconfig +++ b/.editorconfig @@ -28,10 +28,6 @@ indent_style = unset [/assets/email*] indent_size = unset -# ignore Readme -[README.md] -indent_style = unset - -# ignore python +# ignore python and markdown [*.{py,md}] indent_style = unset diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index c13f8d82..1c3a0658 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/airr - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/airrflow/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/airrflow _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`). +- [ ] 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. - [ ] Output Documentation in `docs/output.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 7462873d..11348d0f 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -8,12 +8,12 @@ on: types: [published] workflow_dispatch: jobs: - run-tower: + run-platform: name: Run AWS full tests if: github.repository == 'nf-core/airrflow' runs-on: ubuntu-latest steps: - - name: Launch workflow via tower + - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) @@ -33,7 +33,7 @@ jobs: - uses: actions/upload-artifact@v4 with: - name: Tower debug log file + name: Seqera Platform debug log file path: | - tower_action_*.log - tower_action_*.json + seqera_platform_action_*.log + seqera_platform_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 869b2ab2..e4d97f6d 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -5,13 +5,13 @@ name: nf-core AWS test on: workflow_dispatch: jobs: - run-tower: + run-platform: name: Run AWS tests if: github.repository == 'nf-core/airrflow' runs-on: ubuntu-latest steps: - # Launch workflow using Tower CLI tool action - - name: Launch workflow via tower + # Launch workflow using Seqera Platform CLI tool action + - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} @@ -27,7 +27,7 @@ jobs: - uses: actions/upload-artifact@v4 with: - name: Tower debug log file + name: Seqera Platform debug log file path: | - tower_action_*.log - tower_action_*.json + seqera_platform_action_*.log + seqera_platform_action_*.json diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2562b15c..bb6179a1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,10 +28,10 @@ jobs: - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 08622fd5..2d20d644 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -14,6 +14,8 @@ on: pull_request: types: - opened + - edited + - synchronize branches: - master pull_request_target: @@ -28,11 +30,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: "3.11" + python-version: "3.12" architecture: "x64" - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 with: @@ -65,8 +70,17 @@ jobs: - name: Inspect download run: tree ./${{ env.REPOTITLE_LOWERCASE }} - - name: Run the downloaded pipeline + - name: Run the downloaded pipeline (stub) + id: stub_run_pipeline + continue-on-error: true env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ 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: ${{ job.steps.stub_run_pipeline.status == failure() }} + env: + NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 8dda78ab..2261f74f 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,9 +32,9 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: 3.11 + python-version: "3.12" - name: Install pre-commit run: pip install pre-commit diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 073e1876..a3fb2541 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,12 +14,12 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - name: Set up Python 3.12 + uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: 3.11 + python-version: "3.12" cache: "pip" - name: Install pre-commit @@ -32,14 +32,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: "3.11" + python-version: "3.12" architecture: "x64" - name: Install dependencies @@ -60,7 +60,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index b706875f..40acc23f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3 + uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index d468aeaa..03ecfcf7 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ 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' ' ')" >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: @@ -25,13 +25,13 @@ jobs: Please see the changelog: ${{ github.event.release.html_url }} - ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics + ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics send-tweet: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: python-version: "3.10" - name: Install dependencies diff --git a/.nf-core.yml b/.nf-core.yml index 3805dc81..d6daa403 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1 +1,2 @@ repository_type: pipeline +nf_core_version: "2.14.0" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index af57081f..4dc0f1dc 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,6 +3,9 @@ repos: rev: "v3.1.0" hooks: - id: prettier + additional_dependencies: + - prettier@3.2.5 + - repo: https://github.com/editorconfig-checker/editorconfig-checker.python rev: "2.7.3" hooks: diff --git a/CHANGELOG.md b/CHANGELOG.md index e3d1b11d..fa01f15b 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). -## v3.2.1dev - [date] +## v4.0 - [date] Initial release of nf-core/airrflow, created with the [nf-core](https://nf-co.re/) template. diff --git a/README.md b/README.md index 50b0aa85..9d84b811 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ [![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/) -[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/airrflow) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/airrflow) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23airrflow-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/airrflow)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 848dc14a..6bf130f8 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,9 @@ report_comment: > - This report has been generated by the nf-core/airrflow + + This report has been generated by the nf-core/airrflow analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. + report_section_order: "nf-core-airrflow-methods-description": order: -1000 diff --git a/conf/base.config b/conf/base.config index 9ad4b703..d09a2bb2 100644 --- a/conf/base.config +++ b/conf/base.config @@ -59,7 +59,4 @@ process { errorStrategy = 'retry' maxRetries = 2 } - withName:CUSTOM_DUMPSOFTWAREVERSIONS { - cache = false - } } diff --git a/conf/modules.config b/conf/modules.config index e3ea8fa6..d203d2b6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -22,14 +22,6 @@ process { ext.args = '--quiet' } - withName: CUSTOM_DUMPSOFTWAREVERSIONS { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - pattern: '*_versions.yml' - ] - } - withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/conf/test.config b/conf/test.config index 61a17277..47cb1082 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,7 +22,7 @@ params { // 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 - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' + input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' // Genome references genome = 'R64-1-1' diff --git a/conf/test_full.config b/conf/test_full.config index 9c410f35..4a7e2ac9 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -17,7 +17,7 @@ params { // Input data for full size test // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' + input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' // Genome references genome = 'R64-1-1' diff --git a/docs/usage.md b/docs/usage.md index 6b80bec1..4091ad29 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -156,6 +156,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) +- `wave` + - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. diff --git a/modules.json b/modules.json index 84475b63..30e22ba7 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", + "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", "installed_by": ["modules"] }, "multiqc": { @@ -26,7 +26,7 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 9e19a74c..d79f1c86 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -25,6 +25,11 @@ process FASTQC { def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } 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') + // FastQC memory value allowed range (100 - 10000) + def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) + """ printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name @@ -33,6 +38,7 @@ process FASTQC { fastqc \\ $args \\ --threads $task.cpus \\ + --memory $fastqc_memory \\ $renamed_files cat <<-END_VERSIONS > versions.yml diff --git a/nextflow.config b/nextflow.config index 789b5684..27ca3852 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,7 +16,8 @@ params { genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - fasta = null// MultiQC options + + // MultiQC options multiqc_config = null multiqc_title = null multiqc_logo = null @@ -24,15 +25,16 @@ params { multiqc_methods_description = null // Boilerplate options - outdir = null - publish_dir_mode = 'copy' - email = null - email_on_fail = null - plaintext_email = false - monochrome_logs = false - hook_url = null - help = false - version = false + outdir = null + publish_dir_mode = 'copy' + email = null + email_on_fail = null + plaintext_email = false + monochrome_logs = false + hook_url = null + help = false + version = false + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' // Config options config_profile_name = null @@ -68,103 +70,109 @@ try { } // Load nf-core/airrflow custom profiles from different institutions. -// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs! -// try { -// includeConfig "${params.custom_config_base}/pipeline/airrflow.config" -// } catch (Exception e) { -// System.err.println("WARNING: Could not load nf-core/config/airrflow profiles: ${params.custom_config_base}/pipeline/airrflow.config") -// } +try { + includeConfig "${params.custom_config_base}/pipeline/airrflow.config" +} catch (Exception e) { + System.err.println("WARNING: Could not load nf-core/config/airrflow profiles: ${params.custom_config_base}/pipeline/airrflow.config") +} profiles { debug { - dumpHashes = true - process.beforeScript = 'echo $HOSTNAME' - cleanup = false + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + cleanup = false nextflow.enable.configProcessNamesValidation = true } conda { - conda.enabled = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - channels = ['conda-forge', 'bioconda', 'defaults'] - apptainer.enabled = false + conda.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + conda.channels = ['conda-forge', 'bioconda', 'defaults'] + apptainer.enabled = false } mamba { - conda.enabled = true - conda.useMamba = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + conda.enabled = true + conda.useMamba = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } docker { - docker.enabled = true - conda.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false - docker.runOptions = '-u $(id -u):$(id -g)' + docker.enabled = true + conda.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false + docker.runOptions = '-u $(id -u):$(id -g)' } arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { - singularity.enabled = true - singularity.autoMounts = true - conda.enabled = false - docker.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + singularity.enabled = true + singularity.autoMounts = true + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } podman { - podman.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + podman.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } shifter { - shifter.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + shifter.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } charliecloud { - charliecloud.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - apptainer.enabled = false + charliecloud.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + apptainer.enabled = false } apptainer { - apptainer.enabled = true - apptainer.autoMounts = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + apptainer.enabled = true + apptainer.autoMounts = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + wave { + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' } gitpod { - executor.name = 'local' - executor.cpus = 4 - executor.memory = 8.GB + executor.name = 'local' + executor.cpus = 4 + executor.memory = 8.GB } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } @@ -231,7 +239,7 @@ manifest { description = """B and T cell repertoire analysis pipeline with the Immcantation framework.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.2.1dev' + version = '4.0' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index b5487767..c36ce188 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -265,6 +265,13 @@ "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", + "description": "Base URL or local path to location of pipeline test dataset files", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", + "hidden": true } } } diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 56110621..00000000 --- a/pyproject.toml +++ /dev/null @@ -1,15 +0,0 @@ -# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff. -# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation. -[tool.ruff] -line-length = 120 -target-version = "py38" -cache-dir = "~/.cache/ruff" - -[tool.ruff.lint] -select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] - -[tool.ruff.lint.isort] -known-first-party = ["nf_core"] - -[tool.ruff.lint.per-file-ignores] -"__init__.py" = ["E402", "F401"] diff --git a/subworkflows/local/utils_nfcore_airrflow_pipeline/main.nf b/subworkflows/local/utils_nfcore_airrflow_pipeline/main.nf index de9642e5..80e2ebc0 100644 --- a/subworkflows/local/utils_nfcore_airrflow_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_airrflow_pipeline/main.nf @@ -140,6 +140,10 @@ workflow PIPELINE_COMPLETION { imNotification(summary_params, hook_url) } } + + workflow.onError { + log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting" + } } /* @@ -230,8 +234,16 @@ def methodsDescriptionText(mqc_methods_yaml) { meta["manifest_map"] = workflow.manifest.toMap() // Pipeline DOI - meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" - 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.
    • " + if (meta.manifest_map.doi) { + // 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 + def temp_doi_ref = "" + String[] manifest_doi = meta.manifest_map.doi.tokenize(",") + for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) + } else meta["doi_text"] = "" + meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " // Tool references meta["tool_citations"] = "" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index a8b55d6f..14558c39 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) { // Citation string for pipeline // def workflowCitation() { + def temp_doi_ref = "" + String[] manifest_doi = workflow.manifest.doi.tokenize(",") + // Using a loop to handle multiple DOIs + // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers + // Removing ` ` since the manifest.doi is a string and not a proper list + for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + - " ${workflow.manifest.doi}\n\n" + + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + diff --git a/workflows/airrflow.nf b/workflows/airrflow.nf index 231ebbd5..a8d29d0d 100644 --- a/workflows/airrflow.nf +++ b/workflows/airrflow.nf @@ -40,22 +40,44 @@ workflow AIRRFLOW { // Collate and save software versions // softwareVersionsToYAML(ch_versions) - .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) - .set { ch_collated_versions } + .collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'nf_core_pipeline_software_mqc_versions.yml', + sort: true, + newLine: true + ).set { ch_collated_versions } // // MODULE: MultiQC // - ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() - ch_multiqc_logo = params.multiqc_logo ? 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_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) + ch_multiqc_config = Channel.fromPath( + "$projectDir/assets/multiqc_config.yml", checkIfExists: true) + ch_multiqc_custom_config = params.multiqc_config ? + Channel.fromPath(params.multiqc_config, checkIfExists: true) : + Channel.empty() + ch_multiqc_logo = params.multiqc_logo ? + 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_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( + name: 'methods_description_mqc.yaml', + sort: true + ) + ) MULTIQC ( ch_multiqc_files.collect(), From 0788d447e7392528d808273b38e14e917cb7e963 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 9 May 2024 11:37:36 +0000 Subject: [PATCH 02/12] Template update for nf-core/tools version 2.14.1 --- .github/workflows/linting.yml | 1 - .nf-core.yml | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index a3fb2541..1fcafe88 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -20,7 +20,6 @@ jobs: uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: python-version: "3.12" - cache: "pip" - name: Install pre-commit run: pip install pre-commit diff --git a/.nf-core.yml b/.nf-core.yml index d6daa403..e0b85a77 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,2 +1,2 @@ repository_type: pipeline -nf_core_version: "2.14.0" +nf_core_version: "2.14.1" From 46f8eb6d183fe6422bcbc00d86b140098849d7ce Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 20 May 2024 18:30:38 -0400 Subject: [PATCH 03/12] try fix report file size --- modules/local/rename_file.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/rename_file.nf b/modules/local/rename_file.nf index 6f99ef89..cc8e7cf6 100644 --- a/modules/local/rename_file.nf +++ b/modules/local/rename_file.nf @@ -16,6 +16,6 @@ process RENAME_FILE { script: """ - mv ${file} ${meta.id}_${file.name} + mv ${file} ${meta.id}.${file.extension} """ } From 4401e8cb6b1537980cd6856145635883a6532211 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 20 May 2024 18:35:21 -0400 Subject: [PATCH 04/12] fix sequence number plot --- assets/repertoire_comparison.Rmd | 3 ++- modules/local/rename_file.nf | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/assets/repertoire_comparison.Rmd b/assets/repertoire_comparison.Rmd index d3f83e75..b16a9cf4 100644 --- a/assets/repertoire_comparison.Rmd +++ b/assets/repertoire_comparison.Rmd @@ -106,8 +106,9 @@ The full table can be found under [Table_sequences_assembled](repertoire_compari ```{r seq_assembled, echo=FALSE, warning=FALSE, results='asis'} tab_seqs_assembled <- read.table("./Table_sequences_assembled.tsv", header=TRUE, sep="\t", check.names = FALSE) +# Splitting on last underscore for sample_id if (any(is.na(tab_seqs_assembled$sample_id))) { - tab_seqs_assembled$sample_id <- sapply(tab_seqs_assembled$file_0, function(x) unlist(strsplit(as.character(x), "_"))[1]) + tab_seqs_assembled$sample_id <- sapply(tab_seqs_assembled$file_0, function(x) unlist(strsplit(as.character(x), "_\\s*(?=[^_]+$)", perl=TRUE))[1]) } dat <- tab_seqs_assembled %>% diff --git a/modules/local/rename_file.nf b/modules/local/rename_file.nf index cc8e7cf6..1988bc98 100644 --- a/modules/local/rename_file.nf +++ b/modules/local/rename_file.nf @@ -12,7 +12,7 @@ process RENAME_FILE { tuple val(meta), path(file) output: - tuple val(meta), path("${meta.id}_${file.name}") , emit: file + tuple val(meta), path("${meta.id}.${file.extension}") , emit: file script: """ From bdaf234f6260aaa83cf9751f16b2d52154f7922c Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 28 May 2024 14:39:57 -0400 Subject: [PATCH 05/12] update changelog --- CHANGELOG.md | 12 ++++++++++++ nextflow.config | 2 +- 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 42b92beb..99cc72b0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,18 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). +## [4.1.0] - + +### `Added` + +- [#335](https://github.com/nf-core/airrflow/pull/319) Update to nf-core template 2.14.1 + +### `Fixed` + +- [#335](https://github.com/nf-core/airrflow/pull/335) Fix report number of sequences per sample plots. + +### `Dependencies` + ## [4.0] - 2024-04-22 Ascendio ### `Added` diff --git a/nextflow.config b/nextflow.config index 00c53278..0f58aa0e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -368,7 +368,7 @@ manifest { description = """B and T cell repertoire analysis pipeline with the Immcantation framework.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '4.0' + version = '4.1.0' doi = '10.5281/zenodo.2642009' } From 50df308aee0b2e8f75467e7ce36a0a1d7d06397c Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 28 May 2024 15:10:58 -0400 Subject: [PATCH 06/12] update testdata base path --- conf/test.config | 10 +++++----- conf/test_10x_sc.config | 4 ++-- conf/test_assembled_hs.config | 6 +++--- conf/test_assembled_immcantation_devel_hs.config | 6 +++--- conf/test_assembled_immcantation_devel_mm.config | 6 +++--- conf/test_assembled_mm.config | 6 +++--- conf/test_clontech_umi.config | 6 +++--- conf/test_fetchimgt.config | 6 +++--- conf/test_full.config | 6 +++--- conf/test_nebnext_umi.config | 6 +++--- conf/test_no_umi.config | 10 +++++----- conf/test_nocluster.config | 10 +++++----- conf/test_raw_immcantation_devel.config | 10 +++++----- conf/test_tcr.config | 10 +++++----- nextflow.config | 4 ++-- 15 files changed, 53 insertions(+), 53 deletions(-) diff --git a/conf/test.config b/conf/test.config index 4d6b1c40..b9b0b19a 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,11 +20,11 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/Metadata_test_airr.tsv' - cprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/C_primers.fasta' - vprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/V_primers.fasta' - reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' - reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv' + cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta' + vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta' + reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' mode = 'fastq' diff --git a/conf/test_10x_sc.config b/conf/test_10x_sc.config index 76936ef9..4eb926b4 100644 --- a/conf/test_10x_sc.config +++ b/conf/test_10x_sc.config @@ -23,6 +23,6 @@ params { // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-sc/10x_sc_raw.tsv' - reference_10x = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-sc/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.tar.gz' + input = pipelines_testdata_base_path + 'airrflow/testdata-sc/10x_sc_raw.tsv' + reference_10x = pipelines_testdata_base_path + 'airrflow/testdata-sc/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.tar.gz' } diff --git a/conf/test_assembled_hs.config b/conf/test_assembled_hs.config index bb6caa19..e8f1462c 100644 --- a/conf/test_assembled_hs.config +++ b/conf/test_assembled_hs.config @@ -18,9 +18,9 @@ params { // Input data mode = 'assembled' - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-reveal/test_assembled_metadata_hs.tsv' - reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' - reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_hs.tsv' + reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' reassign = true productive_only = true diff --git a/conf/test_assembled_immcantation_devel_hs.config b/conf/test_assembled_immcantation_devel_hs.config index da5c8d56..adc0332b 100644 --- a/conf/test_assembled_immcantation_devel_hs.config +++ b/conf/test_assembled_immcantation_devel_hs.config @@ -18,9 +18,9 @@ params { // Input data mode = 'assembled' - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-reveal/test_assembled_metadata_hs.tsv' - reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' - reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_hs.tsv' + reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' reassign = true productive_only = true diff --git a/conf/test_assembled_immcantation_devel_mm.config b/conf/test_assembled_immcantation_devel_mm.config index 33fd5bcb..3bc602ea 100644 --- a/conf/test_assembled_immcantation_devel_mm.config +++ b/conf/test_assembled_immcantation_devel_mm.config @@ -18,9 +18,9 @@ params { // Input data mode = 'assembled' - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-reveal/test_assembled_metadata_mm.tsv' - reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' - reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_mm.tsv' + reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' reassign = true productive_only = true diff --git a/conf/test_assembled_mm.config b/conf/test_assembled_mm.config index 69ad5052..f90e7319 100644 --- a/conf/test_assembled_mm.config +++ b/conf/test_assembled_mm.config @@ -18,9 +18,9 @@ params { // Input data mode = 'assembled' - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-reveal/test_assembled_metadata_mm.tsv' - reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' - reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_mm.tsv' + reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' reassign = true productive_only = true diff --git a/conf/test_clontech_umi.config b/conf/test_clontech_umi.config index 1d64ad1c..55dda02a 100644 --- a/conf/test_clontech_umi.config +++ b/conf/test_clontech_umi.config @@ -21,10 +21,10 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-clontech/samplesheet.tsv' + input = pipelines_testdata_base_path +'airrflow/testdata-clontech/samplesheet.tsv' - reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' - reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' + reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' clonal_threshold = 0.1 diff --git a/conf/test_fetchimgt.config b/conf/test_fetchimgt.config index cc6608f7..14431d1b 100644 --- a/conf/test_fetchimgt.config +++ b/conf/test_fetchimgt.config @@ -20,9 +20,9 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/Metadata_test_airr.tsv' - cprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/C_primers.fasta' - vprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/V_primers.fasta' + input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv' + cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta' + vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta' fetch_imgt = true mode = 'fastq' diff --git a/conf/test_full.config b/conf/test_full.config index 0ac79d53..f6146bcf 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,11 +15,11 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/metadata_pcr_umi_airr_300.tsv' + input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/metadata_pcr_umi_airr_300.tsv' cprimers = 's3://ngi-igenomes/test-data/airrflow/pcr_umi/cprimers.fasta' vprimers = 's3://ngi-igenomes/test-data/airrflow/pcr_umi/vprimers.fasta' - reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' - reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' + reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' lineage_trees = true diff --git a/conf/test_nebnext_umi.config b/conf/test_nebnext_umi.config index 76c9bbea..ff7c22d8 100644 --- a/conf/test_nebnext_umi.config +++ b/conf/test_nebnext_umi.config @@ -22,10 +22,10 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-neb/samplesheet.tsv' + input = pipelines_testdata_base_path + 'airrflow/testdata-neb/samplesheet.tsv' - reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' - reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' + reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' clonal_threshold = 0.1 diff --git a/conf/test_no_umi.config b/conf/test_no_umi.config index 8800b20c..b694e796 100644 --- a/conf/test_no_umi.config +++ b/conf/test_no_umi.config @@ -27,11 +27,11 @@ params { isotype_column = 'c_primer' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-no-umi/Metadata_test-no-umi_airr.tsv' - cprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-no-umi/Greiff2014_CPrimers.fasta' - vprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-no-umi/Greiff2014_VPrimers.fasta' - reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' - reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'airrflow/testdata-no-umi/Metadata_test-no-umi_airr.tsv' + cprimers = pipelines_testdata_base_path + 'airrflow/testdata-no-umi/Greiff2014_CPrimers.fasta' + vprimers = pipelines_testdata_base_path + 'airrflow/testdata-no-umi/Greiff2014_VPrimers.fasta' + reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' } diff --git a/conf/test_nocluster.config b/conf/test_nocluster.config index aabccb9b..c1b3d10b 100644 --- a/conf/test_nocluster.config +++ b/conf/test_nocluster.config @@ -20,11 +20,11 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/Metadata_test_airr.tsv' - cprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/C_primers.fasta' - vprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/V_primers.fasta' - reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' - reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv' + cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta' + vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta' + reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' mode = 'fastq' diff --git a/conf/test_raw_immcantation_devel.config b/conf/test_raw_immcantation_devel.config index 11b8ff69..a897d1ce 100644 --- a/conf/test_raw_immcantation_devel.config +++ b/conf/test_raw_immcantation_devel.config @@ -20,12 +20,12 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/Metadata_test_airr.tsv' - cprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/C_primers.fasta' - vprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/V_primers.fasta' + input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv' + cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta' + vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta' - reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' - reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' + reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' mode = 'fastq' diff --git a/conf/test_tcr.config b/conf/test_tcr.config index 5af84ee7..a178ba5d 100644 --- a/conf/test_tcr.config +++ b/conf/test_tcr.config @@ -28,11 +28,11 @@ params { // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-tcr/TCR_metadata_airr.tsv' - cprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-tcr/cprimers.fasta' - race_linker = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-tcr/linker.fasta' - reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' - reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' + input = pipelines_testdata_base_path + 'airrflow/testdata-tcr/TCR_metadata_airr.tsv' + cprimers = pipelines_testdata_base_path + 'airrflow/testdata-tcr/cprimers.fasta' + race_linker = pipelines_testdata_base_path + 'airrflow/testdata-tcr/linker.fasta' + reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip' } diff --git a/nextflow.config b/nextflow.config index d4b87c2d..cf42dd39 100644 --- a/nextflow.config +++ b/nextflow.config @@ -81,8 +81,8 @@ params { // ----------------------- productive_only = true reassign = true - reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' - reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' + reference_igblast = "${params.pipelines_testdata_base_path}airrflow/database-cache/igblast_base.zip" + reference_fasta = "${pipelines_testdata_base_path}airrflow/database-cache/imgtdb_base.zip" fetch_imgt = false save_databases = true isotype_column = 'c_call' From 22f410debe374a2005592e88a11a5a5712365304 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 28 May 2024 15:22:05 -0400 Subject: [PATCH 07/12] rm custom software versions --- conf/base.config | 3 --- conf/modules.config | 8 -------- 2 files changed, 11 deletions(-) diff --git a/conf/base.config b/conf/base.config index 4f304f7e..6606bdac 100644 --- a/conf/base.config +++ b/conf/base.config @@ -61,7 +61,4 @@ process { cpus = { check_max( 16 * task.attempt, 'cpus' ) } memory = { check_max( 72.GB * task.attempt, 'memory' ) } } - withName:CUSTOM_DUMPSOFTWAREVERSIONS { - cache = false - } } diff --git a/conf/modules.config b/conf/modules.config index 3bfdc09f..3dc63fa9 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,14 +18,6 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: CUSTOM_DUMPSOFTWAREVERSIONS { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - pattern: '*_versions.yml' - ] - } - // Validate input raw withName: SAMPLESHEET_CHECK { publishDir = [ From ee7c2642e170a1ab48c44fb86a11d03d0910cbaf Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 28 May 2024 15:22:28 -0400 Subject: [PATCH 08/12] solve warning --- subworkflows/local/presto_umi.nf | 44 ++++++++++++++++---------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/subworkflows/local/presto_umi.nf b/subworkflows/local/presto_umi.nf index 89e8d5f6..17caa68e 100644 --- a/subworkflows/local/presto_umi.nf +++ b/subworkflows/local/presto_umi.nf @@ -7,28 +7,28 @@ include { FASTP } from '../../modules/n //PRESTO -include { PRESTO_FILTERSEQ as PRESTO_FILTERSEQ_UMI } from '../../modules/local/presto/presto_filterseq' -include { PRESTO_MASKPRIMERS as PRESTO_MASKPRIMERS_UMI } from '../../modules/local/presto/presto_maskprimers' -include { PRESTO_MASKPRIMERS_ALIGN } from '../../modules/local/presto/presto_maskprimers_align' -include { PRESTO_MASKPRIMERS_EXTRACT } from '../../modules/local/presto/presto_maskprimers_extract' -include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_ALIGN_CREGION } from '../../modules/local/presto/presto_maskprimers_align' -include { PRESTO_PAIRSEQ as PRESTO_PAIRSEQ_UMI } from '../../modules/local/presto/presto_pairseq' -include { PRESTO_PAIRSEQ as PRESTO_PAIRSEQ_ALIGN } from '../../modules/local/presto/presto_pairseq' -include { PRESTO_CLUSTERSETS as PRESTO_CLUSTERSETS_UMI } from '../../modules/local/presto/presto_clustersets' -include { PRESTO_PARSE_CLUSTER as PRESTO_PARSE_CLUSTER_UMI } from '../../modules/local/presto/presto_parse_cluster' -include { PRESTO_BUILDCONSENSUS as PRESTO_BUILDCONSENSUS_UMI } from '../../modules/local/presto/presto_buildconsensus' -include { PRESTO_BUILDCONSENSUS as PRESTO_BUILDCONSENSUS_ALIGN } from '../../modules/local/presto/presto_buildconsensus' +include { PRESTO_FILTERSEQ as PRESTO_FILTERSEQ_UMI } from '../../modules/local/presto/presto_filterseq' +include { PRESTO_MASKPRIMERS as PRESTO_MASKPRIMERS_UMI } from '../../modules/local/presto/presto_maskprimers' +include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_ALIGN_PRIMERS } from '../../modules/local/presto/presto_maskprimers_align' +include { PRESTO_MASKPRIMERS_EXTRACT } from '../../modules/local/presto/presto_maskprimers_extract' +include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_ALIGN_CREGION } from '../../modules/local/presto/presto_maskprimers_align' +include { PRESTO_PAIRSEQ as PRESTO_PAIRSEQ_UMI } from '../../modules/local/presto/presto_pairseq' +include { PRESTO_PAIRSEQ as PRESTO_PAIRSEQ_ALIGN } from '../../modules/local/presto/presto_pairseq' +include { PRESTO_CLUSTERSETS as PRESTO_CLUSTERSETS_UMI } from '../../modules/local/presto/presto_clustersets' +include { PRESTO_PARSE_CLUSTER as PRESTO_PARSE_CLUSTER_UMI } from '../../modules/local/presto/presto_parse_cluster' +include { PRESTO_BUILDCONSENSUS as PRESTO_BUILDCONSENSUS_UMI} from '../../modules/local/presto/presto_buildconsensus' +include { PRESTO_BUILDCONSENSUS as PRESTO_BUILDCONSENSUS_ALIGN } from '../../modules/local/presto/presto_buildconsensus' include { PRESTO_POSTCONSENSUS_PAIRSEQ as PRESTO_POSTCONSENSUS_PAIRSEQ_UMI } from '../../modules/local/presto/presto_postconsensus_pairseq' -include { PRESTO_ASSEMBLEPAIRS as PRESTO_ASSEMBLEPAIRS_UMI } from '../../modules/local/presto/presto_assemblepairs' -include { PRESTO_ASSEMBLEPAIRS_SEQUENTIAL } from '../../modules/local/presto/presto_assemblepairs_sequential' +include { PRESTO_ASSEMBLEPAIRS as PRESTO_ASSEMBLEPAIRS_UMI } from '../../modules/local/presto/presto_assemblepairs' +include { PRESTO_ASSEMBLEPAIRS_SEQUENTIAL } from '../../modules/local/presto/presto_assemblepairs_sequential' include { PRESTO_PARSEHEADERS as PRESTO_PARSEHEADERS_COLLAPSE_UMI } from '../../modules/local/presto/presto_parseheaders' -include { PRESTO_PARSEHEADERS as PRESTO_PARSEHEADERS_CREGION } from '../../modules/local/presto/presto_parseheaders' +include { PRESTO_PARSEHEADERS as PRESTO_PARSEHEADERS_CREGION } from '../../modules/local/presto/presto_parseheaders' include { PRESTO_PARSEHEADERS_PRIMERS as PRESTO_PARSEHEADERS_PRIMERS_UMI } from '../../modules/local/presto/presto_parseheaders_primers' include { PRESTO_PARSEHEADERS_METADATA as PRESTO_PARSEHEADERS_METADATA_UMI } from '../../modules/local/presto/presto_parseheaders_metadata' -include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_UMI } from '../../modules/local/presto/presto_collapseseq' -include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_ALIGN } from '../../modules/local/presto/presto_collapseseq' -include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_CREGION } from '../../modules/local/presto/presto_collapseseq' -include { PRESTO_SPLITSEQ as PRESTO_SPLITSEQ_UMI} from '../../modules/local/presto/presto_splitseq' +include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_UMI } from '../../modules/local/presto/presto_collapseseq' +include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_ALIGN } from '../../modules/local/presto/presto_collapseseq' +include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_CREGION} from '../../modules/local/presto/presto_collapseseq' +include { PRESTO_SPLITSEQ as PRESTO_SPLITSEQ_UMI } from '../../modules/local/presto/presto_splitseq' workflow PRESTO_UMI { @@ -108,7 +108,7 @@ workflow PRESTO_UMI { .map{ reads -> [reads[0], reads[1]] }.dump(tag: 'ch_reads_R1') ch_reads_R2 = PRESTO_FILTERSEQ_UMI.out.reads .map{ reads -> [reads[0], reads[2]] }.dump(tag: 'ch_reads_R2') - PRESTO_MASKPRIMERS_ALIGN( + PRESTO_ALIGN_PRIMERS( ch_reads_R1, ch_cprimers.collect(), params.primer_maxlen, @@ -119,15 +119,15 @@ workflow PRESTO_UMI { ch_reads_R2 ) - ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_ALIGN.out.versions) + ch_versions = ch_versions.mix(PRESTO_ALIGN_PRIMERS.out.versions) ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_EXTRACT.out.versions) // Merge again R1 and R2 by sample ID. - ch_maskprimers_reads_R1 = PRESTO_MASKPRIMERS_ALIGN.out.reads.map{ reads -> [reads[0].id, reads[0], reads[1]]}.dump(tag: 'ch_maskprimers_reads_R1') + ch_maskprimers_reads_R1 = PRESTO_ALIGN_PRIMERS.out.reads.map{ reads -> [reads[0].id, reads[0], reads[1]]}.dump(tag: 'ch_maskprimers_reads_R1') ch_maskprimers_reads_R2 = PRESTO_MASKPRIMERS_EXTRACT.out.reads.map{ reads -> [reads[0].id, reads[0], reads[1]]}.dump(tag: 'ch_maskprimers_reads_R2') ch_maskprimers_reads = ch_maskprimers_reads_R1.join(ch_maskprimers_reads_R2) .map{ it -> [it[1], it[2], it[4]] }.dump(tag: 'ch_maskprimers_reads_after_remerge') - ch_maskprimers_logs = PRESTO_MASKPRIMERS_ALIGN.out.logs + ch_maskprimers_logs = PRESTO_ALIGN_PRIMERS.out.logs ch_maskprimers_logs = ch_maskprimers_logs.mix(PRESTO_MASKPRIMERS_EXTRACT.out.logs) PRESTO_PAIRSEQ_ALIGN( ch_maskprimers_reads ) From 140cc54cf3d48fdc3af10bd2c8499e9260fc69d3 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 28 May 2024 16:05:59 -0400 Subject: [PATCH 09/12] fix testdata path param --- nextflow.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index cf42dd39..eab84849 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,6 +14,7 @@ params { mode = "fastq" miairr="$projectDir/assets/reveal/mapping_MiAIRR_BioSample_v1.3.1.tsv" index_file = false + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' // ---------------------------- @@ -82,7 +83,7 @@ params { productive_only = true reassign = true reference_igblast = "${params.pipelines_testdata_base_path}airrflow/database-cache/igblast_base.zip" - reference_fasta = "${pipelines_testdata_base_path}airrflow/database-cache/imgtdb_base.zip" + reference_fasta = "${params.pipelines_testdata_base_path}airrflow/database-cache/imgtdb_base.zip" fetch_imgt = false save_databases = true isotype_column = 'c_call' @@ -150,7 +151,6 @@ params { hook_url = null help = false version = false - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' // Config options config_profile_name = null From 69c626f7c1d5b480813ed9f54cef7395f0996389 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 28 May 2024 17:01:31 -0400 Subject: [PATCH 10/12] rm monochromelog warning --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index eab84849..60a4edb4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -15,6 +15,7 @@ params { miairr="$projectDir/assets/reveal/mapping_MiAIRR_BioSample_v1.3.1.tsv" index_file = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' + monochromeLogs = false // ---------------------------- From 967b3b7db5af58dfe296acb686db57821e2a5309 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 28 May 2024 18:10:42 -0400 Subject: [PATCH 11/12] update old container biopython --- CHANGELOG.md | 4 ++++ modules/local/merge_UMI.nf | 6 +++--- modules/local/rename_fastq.nf | 6 +++--- modules/local/rename_file.nf | 6 +++--- 4 files changed, 13 insertions(+), 9 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 99cc72b0..2689754a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Dependencies` +| Dependency | Old version | New version | +| ---------- | ----------- | ----------- | +| biopython | 1.71 | 1.81 | + ## [4.0] - 2024-04-22 Ascendio ### `Added` diff --git a/modules/local/merge_UMI.nf b/modules/local/merge_UMI.nf index a92ef4fe..a90957b1 100644 --- a/modules/local/merge_UMI.nf +++ b/modules/local/merge_UMI.nf @@ -3,10 +3,10 @@ process MERGE_UMI { tag "$meta.id" label 'process_low' - conda "conda-forge::python=3.8.0 conda-forge::biopython=1.74" + conda "conda-forge::biopython=1.81" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-adc9bb9edc31eb38b3c24786a83b7dfa530e2bea:47d6d7765d7537847ced7dac873190d164146022-0' : - 'biocontainers/mulled-v2-adc9bb9edc31eb38b3c24786a83b7dfa530e2bea:47d6d7765d7537847ced7dac873190d164146022-0' }" + 'https://depot.galaxyproject.org/singularity/biopython:1.81' : + 'biocontainers/biopython:1.81' }" input: tuple val(meta), path(R1), path(R2), path(I1) diff --git a/modules/local/rename_fastq.nf b/modules/local/rename_fastq.nf index 012f8f0b..0b8d655b 100644 --- a/modules/local/rename_fastq.nf +++ b/modules/local/rename_fastq.nf @@ -3,10 +3,10 @@ process RENAME_FASTQ { tag "$meta.id" label 'process_low' - conda "conda-forge::python=3.8.0 conda-forge::biopython=1.74" + conda "conda-forge::biopython=1.81" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-adc9bb9edc31eb38b3c24786a83b7dfa530e2bea:47d6d7765d7537847ced7dac873190d164146022-0' : - 'biocontainers/mulled-v2-adc9bb9edc31eb38b3c24786a83b7dfa530e2bea:47d6d7765d7537847ced7dac873190d164146022-0' }" + 'https://depot.galaxyproject.org/singularity/biopython:1.81' : + 'biocontainers/biopython:1.81' }" input: tuple val(meta), path(R1), path(R2) diff --git a/modules/local/rename_file.nf b/modules/local/rename_file.nf index 1988bc98..786d93e5 100644 --- a/modules/local/rename_file.nf +++ b/modules/local/rename_file.nf @@ -3,10 +3,10 @@ process RENAME_FILE { tag "$meta.id" label 'process_low' - conda "conda-forge::python=3.8.0 conda-forge::biopython=1.74" + conda "conda-forge::biopython=1.81" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-adc9bb9edc31eb38b3c24786a83b7dfa530e2bea:47d6d7765d7537847ced7dac873190d164146022-0' : - 'biocontainers/mulled-v2-adc9bb9edc31eb38b3c24786a83b7dfa530e2bea:47d6d7765d7537847ced7dac873190d164146022-0' }" + 'https://depot.galaxyproject.org/singularity/biopython:1.81' : + 'biocontainers/biopython:1.81' }" input: tuple val(meta), path(file) From 094f254b59bc72dabdc2c29a09853f8ed0328f35 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 28 May 2024 18:20:27 -0400 Subject: [PATCH 12/12] revert monochrome logs as nf-core lint fails --- nextflow.config | 2 -- 1 file changed, 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 60a4edb4..3dfaec00 100644 --- a/nextflow.config +++ b/nextflow.config @@ -15,8 +15,6 @@ params { miairr="$projectDir/assets/reveal/mapping_MiAIRR_BioSample_v1.3.1.tsv" index_file = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - monochromeLogs = false - // ---------------------------- // sequencing protocol options