From c081571d72a49f8295f8bf8fdb08cbf60a2d5ea6 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Wed, 17 Jan 2024 11:30:25 +0000 Subject: [PATCH 01/72] Rename cloudtest back to awstest --- .github/workflows/{cloudtest.yml => awstest.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{cloudtest.yml => awstest.yml} (100%) diff --git a/.github/workflows/cloudtest.yml b/.github/workflows/awstest.yml similarity index 100% rename from .github/workflows/cloudtest.yml rename to .github/workflows/awstest.yml From 79fd632bf4cda5aae548e6a0370f1809ef30777f Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Wed, 17 Jan 2024 11:47:28 +0000 Subject: [PATCH 02/72] Change logic of cloud tests workflow --- .github/workflows/awstest.yml | 71 ++++++++++++++--------------------- 1 file changed, 29 insertions(+), 42 deletions(-) diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 829d870ff5..bf518d743e 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -39,71 +39,58 @@ jobs: matrix: include: - profile: test_aws - enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.test && inputs.aws ) ) }} + enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.test && inputs.aws ) ) }} + compute_env: TOWER_COMPUTE_ENV + workdir: TOWER_BUCKET_AWS - profile: test_azure - enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.test && inputs.azure ) ) }} + enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.test && inputs.azure ) ) }} + compute_env: TOWER_CE_AZURE_CPU + workdir: TOWER_BUCKET_AZURE - profile: test_full_aws - enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.somatic && inputs.aws ) ) }} + enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.somatic && inputs.aws ) ) }} + compute_env: TOWER_COMPUTE_ENV + workdir: TOWER_BUCKET_AWS - profile: test_full_azure - enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.somatic && inputs.azure ) ) }} + enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.somatic && inputs.azure ) ) }} + compute_env: TOWER_CE_AZURE_CPU + workdir: TOWER_BUCKET_AZURE - profile: test_full_germline_aws - enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.aws ) ) }} + enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.aws ) ) }} + compute_env: TOWER_COMPUTE_ENV + workdir: TOWER_BUCKET_AWS - profile: test_full_germline_azure - enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.azure ) ) }} - - profile: test_full_germline_ncbench_agilent_aws - enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline_ncbench_agilent && inputs.aws ) ) }} + enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.azure ) ) }} + compute_env: TOWER_CE_AZURE_CPU + workdir: TOWER_BUCKET_AZURE + - profile: test_full_germline_ncbench_agilent + enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.germline_ncbench_agilent && inputs.aws ) ) }} + compute_env: TOWER_COMPUTE_ENV + workdir: TOWER_BUCKET_AWS steps: # Launch workflow on AWS Batch - - name: AWS Launch + - name: Launch uses: seqeralabs/action-tower-launch@v2 - if: ${{ matrix.enabled && ( github.event_name != 'workflow_dispatch' || inputs.aws ) }} + if: ${{ matrix.enabled }} with: run_name: sarek_${{ matrix.profile }} workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + compute_env: ${{ secrets[matrix.compute_env] }} revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}/${{ matrix.profile }} + workdir: ${{ secrets[matrix.workdir] }}/work/sarek/work-${{ github.sha }}/${{ matrix.profile }} parameters: | { "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/" + "outdir": "${{ secrets[matrix.workdir] }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/" } profiles: ${{ matrix.profile }} - uses: actions/upload-artifact@v3 - name: Save AWS Logs + name: Save Logs if: success() || failure() with: - name: tower-aws-${{ matrix.profile }}-log - path: | - tower_action_*.log - tower_action_*.json - - # Launch workflow using Tower CLI tool action - - name: Azure Launch - uses: seqeralabs/action-tower-launch@v2 - if: ${{ matrix.enabled && ( github.event_name != 'workflow_dispatch' || inputs.azure ) }} - with: - run_name: sarek_${{ matrix.profile }} - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }} - revision: ${{ github.sha }} - workdir: ${{ secrets.TOWER_BUCKET_AZURE}}/sarek/work-${{ github.sha }}/${{ matrix.profile }} - parameters: | - { - "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", - "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/" - } - profiles: ${{ matrix.profile }} - - - uses: actions/upload-artifact@v3 - name: Save Azure Logs - if: success() || failure() - with: - name: tower-azure-${{ matrix.profile }}-log + name: tower-${{ matrix.profile }}-log path: | tower_action_*.log tower_action_*.json From 7c81a4a5efdefc147e8fbb104263d733f4fefa32 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Wed, 17 Jan 2024 11:56:10 +0000 Subject: [PATCH 03/72] fixup --- .github/workflows/awstest.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index bf518d743e..0e1fbd504f 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -31,8 +31,8 @@ on: default: true jobs: - trigger-profile-test: - name: Run AWS tests + trigger-test: + name: launch runs-on: ubuntu-latest strategy: fail-fast: false From 5b2cad0ce2a97950917d3e765d1df27bd6c5659a Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Wed, 17 Jan 2024 12:07:07 +0000 Subject: [PATCH 04/72] Add repo protection back in --- .github/workflows/awstest.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 0e1fbd504f..6fa4b9a855 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -71,7 +71,7 @@ jobs: # Launch workflow on AWS Batch - name: Launch uses: seqeralabs/action-tower-launch@v2 - if: ${{ matrix.enabled }} + if: ${{ matrix.enabled }} && ${{ github.repository == 'nf-core/sarek'}} with: run_name: sarek_${{ matrix.profile }} workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} From e2778aa567007cfd75b40a4f66abe1ed818448fb Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 17 Jan 2024 12:09:36 +0000 Subject: [PATCH 05/72] [automated] Fix linting with Prettier --- .devcontainer/devcontainer.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe335..4a9bc5c79d 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -18,11 +18,11 @@ "python.linting.flake8Path": "/opt/conda/bin/flake8", "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" + "python.linting.pylintPath": "/opt/conda/bin/pylint", }, // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] - } - } + "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"], + }, + }, } From 0420159bedb82acd329d3c98770d74d3bca1ba96 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Wed, 17 Jan 2024 12:21:18 +0000 Subject: [PATCH 06/72] Change logic of if statement in cloud tests --- .github/workflows/awstest.yml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 6fa4b9a855..63d4afc28e 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -51,19 +51,19 @@ jobs: compute_env: TOWER_COMPUTE_ENV workdir: TOWER_BUCKET_AWS - profile: test_full_azure - enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.somatic && inputs.azure ) ) }} + enabled: ${{ ( inputs.somatic && inputs.azure ) }} compute_env: TOWER_CE_AZURE_CPU workdir: TOWER_BUCKET_AZURE - profile: test_full_germline_aws - enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.aws ) ) }} + enabled: ${{ ( inputs.germline && inputs.aws ) }} compute_env: TOWER_COMPUTE_ENV workdir: TOWER_BUCKET_AWS - profile: test_full_germline_azure - enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.azure ) ) }} + enabled: ${{ ( inputs.germline && inputs.azure ) }} compute_env: TOWER_CE_AZURE_CPU workdir: TOWER_BUCKET_AZURE - profile: test_full_germline_ncbench_agilent - enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.germline_ncbench_agilent && inputs.aws ) ) }} + enabled: ${{ ( inputs.germline_ncbench_agilent && inputs.aws ) }} compute_env: TOWER_COMPUTE_ENV workdir: TOWER_BUCKET_AWS @@ -71,7 +71,8 @@ jobs: # Launch workflow on AWS Batch - name: Launch uses: seqeralabs/action-tower-launch@v2 - if: ${{ matrix.enabled }} && ${{ github.repository == 'nf-core/sarek'}} + # If workflow_dispatch AND matrix.enabled, plus repository protection + if: ( github.event_name != 'workflow_dispatch' || ${{ matrix.enabled }} ) && ${{ github.repository == 'nf-core/sarek' }} with: run_name: sarek_${{ matrix.profile }} workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} From 334782319f63ee1f22f60039cb598edaee5ae32d Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Wed, 17 Jan 2024 12:37:12 +0000 Subject: [PATCH 07/72] Trying contains statement --- .github/workflows/awstest.yml | 24 ++++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 63d4afc28e..5a7947c289 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -34,36 +34,44 @@ jobs: trigger-test: name: launch runs-on: ubuntu-latest + if: ${{ github.repository == 'nf-core/sarek' }} strategy: fail-fast: false matrix: include: - profile: test_aws - enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.test && inputs.aws ) ) }} + test: test + cloud: aws compute_env: TOWER_COMPUTE_ENV workdir: TOWER_BUCKET_AWS - profile: test_azure - enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.test && inputs.azure ) ) }} + test: test + cloud: azure compute_env: TOWER_CE_AZURE_CPU workdir: TOWER_BUCKET_AZURE - profile: test_full_aws - enabled: ${{ ( github.event_name != 'workflow_dispatch' || ( inputs.somatic && inputs.aws ) ) }} + test: somatic + cloud: aws compute_env: TOWER_COMPUTE_ENV workdir: TOWER_BUCKET_AWS - profile: test_full_azure - enabled: ${{ ( inputs.somatic && inputs.azure ) }} + test: somatic + cloud: azure compute_env: TOWER_CE_AZURE_CPU workdir: TOWER_BUCKET_AZURE - profile: test_full_germline_aws - enabled: ${{ ( inputs.germline && inputs.aws ) }} + test: germline + cloud: aws compute_env: TOWER_COMPUTE_ENV workdir: TOWER_BUCKET_AWS - profile: test_full_germline_azure - enabled: ${{ ( inputs.germline && inputs.azure ) }} + test: germline + cloud: azure compute_env: TOWER_CE_AZURE_CPU workdir: TOWER_BUCKET_AZURE - profile: test_full_germline_ncbench_agilent - enabled: ${{ ( inputs.germline_ncbench_agilent && inputs.aws ) }} + test: germline_ncbench_agilent + cloud: aws compute_env: TOWER_COMPUTE_ENV workdir: TOWER_BUCKET_AWS @@ -72,7 +80,7 @@ jobs: - name: Launch uses: seqeralabs/action-tower-launch@v2 # If workflow_dispatch AND matrix.enabled, plus repository protection - if: ( github.event_name != 'workflow_dispatch' || ${{ matrix.enabled }} ) && ${{ github.repository == 'nf-core/sarek' }} + if: ( !contains(inputs[matrix.test], 'false') && !contains(inputs[matrix.cloud], 'false') ) with: run_name: sarek_${{ matrix.profile }} workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} From 2aff87ca6e31887cb5daaa649f076bd77aa0b0fd Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Wed, 17 Jan 2024 12:38:39 +0000 Subject: [PATCH 08/72] Add comments| --- .github/workflows/awstest.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 5a7947c289..546634c42e 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -79,7 +79,8 @@ jobs: # Launch workflow on AWS Batch - name: Launch uses: seqeralabs/action-tower-launch@v2 - # If workflow_dispatch AND matrix.enabled, plus repository protection + # If inputs item exists (i.e. workflow_dispatch), then we find matrix.test and check it is false + # If is false, we negate and run the job if: ( !contains(inputs[matrix.test], 'false') && !contains(inputs[matrix.cloud], 'false') ) with: run_name: sarek_${{ matrix.profile }} From a328f6d87735b791446c2fbdd075e4323e72ea3b Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Wed, 17 Jan 2024 13:03:06 +0000 Subject: [PATCH 09/72] CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 824f616280..0577dbe1a4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1351](https://github.com/nf-core/sarek/pull/1351) - Fix params name for test profiles (`bcftools_annotations`) - [#1357](https://github.com/nf-core/sarek/pull/1364) - Fixed bug where samples were dropped while reconstituting BAM files - [#1373](https://github.com/nf-core/sarek/pull/1373) - Add `chr` prefix to NCBench bed file & enable trimming +- [#1378](https://github.com/nf-core/sarek/pull/1378) - Improve cloud tests launch workflow to use matrix ### Removed From 3fd14c2b487c84bf1ee32df3c05d7489fc35a21b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 22 Apr 2024 13:22:57 +0200 Subject: [PATCH 10/72] feat(dev): bump to 3.5.0dev and restart dev on dev branch --- CHANGELOG.md | 18 ++++++++++++++++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 21 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7d1434d995..04ce033eb5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,24 @@ All notable changes to this project will be documented in this file. 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). +## [dev](https://github.com/nf-core/sarek/tree/dev) - Unreleased + +### Added + +### Changed + +- [#1477](https://github.com/nf-core/sarek/pull/1477) - Back to dev + +### Fixed + +### Removed + +### Dependencies + +### Modules / Subworkflows + +### Parameters + ## [3.4.1](https://github.com/nf-core/sarek/releases/tag/3.4.1) - Balgattjåhkkå Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the other one being Pårtetjåkko (Bårddetjåhkkå). diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 20fec4d67b..ce1a6e388e 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/sarek/ custom_logo_title: "nf-core/sarek" report_comment: > - This report has been generated by the nf-core/sarek + This report has been generated by the nf-core/sarek analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-sarek-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index a5526b67ce..ad8093c859 100644 --- a/nextflow.config +++ b/nextflow.config @@ -390,7 +390,7 @@ manifest { description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.4.1' + version = '3.5.0dev' doi = '10.12688/f1000research.16665.2, 10.1101/2023.07.19.549462, 10.5281/zenodo.3476425' } From 7843389e453f7d0fefa98dbcf2a5ae7183666844 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 24 Apr 2024 20:50:12 +0200 Subject: [PATCH 11/72] feat(nf-prov): pin nf-prov to 1.2.2 --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index ad8093c859..f5eb354c9e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -330,7 +330,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet - id 'nf-prov' // Provenance reports for pipeline runs + id 'nf-prov@1.2.2' // Provenance reports for pipeline runs } // Load igenomes.config if required From f2e082c6deab0ec9b985b1bddb29ee893c6024f9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 25 Apr 2024 10:57:18 +0200 Subject: [PATCH 12/72] feat(CHANGELOG): update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 04ce033eb5..fbf548e189 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - [#1477](https://github.com/nf-core/sarek/pull/1477) - Back to dev +- [#1482](https://github.com/nf-core/sarek/pull/1482) - Pin `nf-prov` plugin to `1.2.2` ### Fixed From f338898065dab3f0a087900313dec283a7d51a3f Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 25 Apr 2024 11:00:59 +0200 Subject: [PATCH 13/72] Update .devcontainer/devcontainer.json --- .devcontainer/devcontainer.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 28a560e554..b290e09017 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -14,7 +14,7 @@ }, // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"], - }, - }, + "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] + } + } } From 1275645c29ea7d9296f580faa54fb06f437c399b Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 25 Apr 2024 10:12:48 +0100 Subject: [PATCH 14/72] Rename awstest to cloudtest --- .github/workflows/{awstest.yml => cloudtest.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{awstest.yml => cloudtest.yml} (100%) diff --git a/.github/workflows/awstest.yml b/.github/workflows/cloudtest.yml similarity index 100% rename from .github/workflows/awstest.yml rename to .github/workflows/cloudtest.yml From 335c8ac4b6320f94c0bb52450b8a243835d0d33e Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Thu, 25 Apr 2024 12:47:46 +0000 Subject: [PATCH 15/72] add new citation --- CHANGELOG.md | 1 + README.md | 2 +- nextflow.config | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5a90595788..3eefe40c78 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1477](https://github.com/nf-core/sarek/pull/1477) - Back to dev - [#1482](https://github.com/nf-core/sarek/pull/1482) - Pin `nf-prov` plugin to `1.2.2` +- [#](https://github.com/nf-core/sarek/pull/) - Update citation for publication ### Fixed diff --git a/README.md b/README.md index fc283ba454..460f333b73 100644 --- a/README.md +++ b/README.md @@ -193,7 +193,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# If you use `nf-core/sarek` for your analysis, please cite the `Sarek` article as follows: -> Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven Nahnsen **Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery** _bioRxiv_ [doi: 10.1101/2023.07.19.549462](https://doi.org/10.1101/2023.07.19.549462). +> Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven Nahnsen **Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery** _ NAR Genomics and Bioinformatics_ Volume 6, Issue 2, June 2024, lqae031, [doi: 10.1093/nargab/lqae031](https://doi.org/10.1093/nargab/lqae031). > Garcia M, Juhos S, Larsson M et al. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved]** _F1000Research_ 2020, 9:63 [doi: 10.12688/f1000research.16665.2](http://dx.doi.org/10.12688/f1000research.16665.2). diff --git a/nextflow.config b/nextflow.config index f5eb354c9e..e32da2cb94 100644 --- a/nextflow.config +++ b/nextflow.config @@ -391,7 +391,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' version = '3.5.0dev' - doi = '10.12688/f1000research.16665.2, 10.1101/2023.07.19.549462, 10.5281/zenodo.3476425' + doi = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425' } // Load modules.config for DSL2 module specific options From dd0809e64dfaebb77f5af61e39398153de92caa5 Mon Sep 17 00:00:00 2001 From: Friederike Hanssen Date: Thu, 25 Apr 2024 14:48:51 +0200 Subject: [PATCH 16/72] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3eefe40c78..c9cd995156 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1477](https://github.com/nf-core/sarek/pull/1477) - Back to dev - [#1482](https://github.com/nf-core/sarek/pull/1482) - Pin `nf-prov` plugin to `1.2.2` -- [#](https://github.com/nf-core/sarek/pull/) - Update citation for publication +- [#1485](https://github.com/nf-core/sarek/pull/1485) - Update citation for publication ### Fixed From c189b6ac247d519ebbf0a3d446d01a8af6ce3298 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Fri, 26 Apr 2024 14:45:51 +0000 Subject: [PATCH 17/72] Updating sentieon modules to 202308.02 --- modules.json | 16 ++++++++-------- .../nf-core/sentieon/applyvarcal/environment.yml | 2 +- modules/nf-core/sentieon/applyvarcal/main.nf | 4 ++-- modules/nf-core/sentieon/bwamem/environment.yml | 2 +- modules/nf-core/sentieon/bwamem/main.nf | 4 ++-- modules/nf-core/sentieon/dedup/environment.yml | 2 +- modules/nf-core/sentieon/dedup/main.nf | 4 ++-- .../sentieon/dnamodelapply/environment.yml | 2 +- modules/nf-core/sentieon/dnamodelapply/main.nf | 4 ++-- .../nf-core/sentieon/dnascope/environment.yml | 2 +- modules/nf-core/sentieon/dnascope/main.nf | 4 ++-- .../nf-core/sentieon/gvcftyper/environment.yml | 2 +- modules/nf-core/sentieon/gvcftyper/main.nf | 4 ++-- .../nf-core/sentieon/haplotyper/environment.yml | 2 +- modules/nf-core/sentieon/haplotyper/main.nf | 4 ++-- modules/nf-core/sentieon/varcal/environment.yml | 2 +- modules/nf-core/sentieon/varcal/main.nf | 4 ++-- 17 files changed, 32 insertions(+), 32 deletions(-) diff --git a/modules.json b/modules.json index a3f3a8fd65..747c53a5f5 100644 --- a/modules.json +++ b/modules.json @@ -391,42 +391,42 @@ }, "sentieon/applyvarcal": { "branch": "master", - "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3", + "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973", "installed_by": ["modules"] }, "sentieon/bwamem": { "branch": "master", - "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3", + "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973", "installed_by": ["modules"] }, "sentieon/dedup": { "branch": "master", - "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3", + "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973", "installed_by": ["modules"] }, "sentieon/dnamodelapply": { "branch": "master", - "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3", + "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973", "installed_by": ["modules"] }, "sentieon/dnascope": { "branch": "master", - "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3", + "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973", "installed_by": ["modules"] }, "sentieon/gvcftyper": { "branch": "master", - "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3", + "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973", "installed_by": ["modules"] }, "sentieon/haplotyper": { "branch": "master", - "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3", + "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973", "installed_by": ["modules"] }, "sentieon/varcal": { "branch": "master", - "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3", + "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973", "installed_by": ["modules"] }, "snpeff/download": { diff --git a/modules/nf-core/sentieon/applyvarcal/environment.yml b/modules/nf-core/sentieon/applyvarcal/environment.yml index c4c11b1f85..0af79bedcd 100644 --- a/modules/nf-core/sentieon/applyvarcal/environment.yml +++ b/modules/nf-core/sentieon/applyvarcal/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::sentieon=202308.01 + - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/applyvarcal/main.nf b/modules/nf-core/sentieon/applyvarcal/main.nf index d1d3435dc9..6e5e863c51 100644 --- a/modules/nf-core/sentieon/applyvarcal/main.nf +++ b/modules/nf-core/sentieon/applyvarcal/main.nf @@ -7,8 +7,8 @@ process SENTIEON_APPLYVARCAL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' : - 'biocontainers/sentieon:202308.01--h43eeafb_0' }" + 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' : + 'biocontainers/sentieon:202308.02--h43eeafb_0' }" input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) diff --git a/modules/nf-core/sentieon/bwamem/environment.yml b/modules/nf-core/sentieon/bwamem/environment.yml index c090bfa5ae..f03db6f8a3 100644 --- a/modules/nf-core/sentieon/bwamem/environment.yml +++ b/modules/nf-core/sentieon/bwamem/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::sentieon=202308.01 + - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf index 230297d087..62693851c3 100644 --- a/modules/nf-core/sentieon/bwamem/main.nf +++ b/modules/nf-core/sentieon/bwamem/main.nf @@ -7,8 +7,8 @@ process SENTIEON_BWAMEM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' : - 'biocontainers/sentieon:202308.01--h43eeafb_0' }" + 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' : + 'biocontainers/sentieon:202308.02--h43eeafb_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sentieon/dedup/environment.yml b/modules/nf-core/sentieon/dedup/environment.yml index 622cf73909..e29cfff3e4 100644 --- a/modules/nf-core/sentieon/dedup/environment.yml +++ b/modules/nf-core/sentieon/dedup/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::sentieon=202308.01 + - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/dedup/main.nf b/modules/nf-core/sentieon/dedup/main.nf index fbcd595f47..5f19ab56d8 100644 --- a/modules/nf-core/sentieon/dedup/main.nf +++ b/modules/nf-core/sentieon/dedup/main.nf @@ -7,8 +7,8 @@ process SENTIEON_DEDUP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' : - 'biocontainers/sentieon:202308.01--h43eeafb_0' }" + 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' : + 'biocontainers/sentieon:202308.02--h43eeafb_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/sentieon/dnamodelapply/environment.yml b/modules/nf-core/sentieon/dnamodelapply/environment.yml index 6d27d44a1d..a2f8819313 100644 --- a/modules/nf-core/sentieon/dnamodelapply/environment.yml +++ b/modules/nf-core/sentieon/dnamodelapply/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::sentieon=202308.01 + - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/dnamodelapply/main.nf b/modules/nf-core/sentieon/dnamodelapply/main.nf index b728a5ec31..9a0c70dc22 100644 --- a/modules/nf-core/sentieon/dnamodelapply/main.nf +++ b/modules/nf-core/sentieon/dnamodelapply/main.nf @@ -7,8 +7,8 @@ process SENTIEON_DNAMODELAPPLY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' : - 'biocontainers/sentieon:202308.01--h43eeafb_0' }" + 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' : + 'biocontainers/sentieon:202308.02--h43eeafb_0' }" input: tuple val(meta), path(vcf), path(idx) diff --git a/modules/nf-core/sentieon/dnascope/environment.yml b/modules/nf-core/sentieon/dnascope/environment.yml index 45c2116c04..e6da2dde3e 100644 --- a/modules/nf-core/sentieon/dnascope/environment.yml +++ b/modules/nf-core/sentieon/dnascope/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::sentieon=202308.01 + - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/dnascope/main.nf b/modules/nf-core/sentieon/dnascope/main.nf index 6adea35eea..0671307ba0 100644 --- a/modules/nf-core/sentieon/dnascope/main.nf +++ b/modules/nf-core/sentieon/dnascope/main.nf @@ -7,8 +7,8 @@ process SENTIEON_DNASCOPE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' : - 'biocontainers/sentieon:202308.01--h43eeafb_0' }" + 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' : + 'biocontainers/sentieon:202308.02--h43eeafb_0' }" input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/sentieon/gvcftyper/environment.yml b/modules/nf-core/sentieon/gvcftyper/environment.yml index 9a8143068a..732e2ca846 100644 --- a/modules/nf-core/sentieon/gvcftyper/environment.yml +++ b/modules/nf-core/sentieon/gvcftyper/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::sentieon=202308.01 + - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/gvcftyper/main.nf b/modules/nf-core/sentieon/gvcftyper/main.nf index 4b5c9df4e3..7539214507 100644 --- a/modules/nf-core/sentieon/gvcftyper/main.nf +++ b/modules/nf-core/sentieon/gvcftyper/main.nf @@ -7,8 +7,8 @@ process SENTIEON_GVCFTYPER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' : - 'biocontainers/sentieon:202308.01--h43eeafb_0' }" + 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' : + 'biocontainers/sentieon:202308.02--h43eeafb_0' }" input: tuple val(meta), path(gvcfs), path(tbis), path(intervals) diff --git a/modules/nf-core/sentieon/haplotyper/environment.yml b/modules/nf-core/sentieon/haplotyper/environment.yml index a3a721cf1d..89108f8e8b 100644 --- a/modules/nf-core/sentieon/haplotyper/environment.yml +++ b/modules/nf-core/sentieon/haplotyper/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::sentieon=202308.01 + - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/haplotyper/main.nf b/modules/nf-core/sentieon/haplotyper/main.nf index 87a9343474..16eb775744 100644 --- a/modules/nf-core/sentieon/haplotyper/main.nf +++ b/modules/nf-core/sentieon/haplotyper/main.nf @@ -7,8 +7,8 @@ process SENTIEON_HAPLOTYPER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' : - 'biocontainers/sentieon:202308.01--h43eeafb_0' }" + 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' : + 'biocontainers/sentieon:202308.02--h43eeafb_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/sentieon/varcal/environment.yml b/modules/nf-core/sentieon/varcal/environment.yml index 93921ff046..481da2ce84 100644 --- a/modules/nf-core/sentieon/varcal/environment.yml +++ b/modules/nf-core/sentieon/varcal/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::sentieon=202308.01 + - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/varcal/main.nf b/modules/nf-core/sentieon/varcal/main.nf index 17a3b71845..aa8847f839 100644 --- a/modules/nf-core/sentieon/varcal/main.nf +++ b/modules/nf-core/sentieon/varcal/main.nf @@ -7,8 +7,8 @@ process SENTIEON_VARCAL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sentieon:202308.01--h43eeafb_0' : - 'biocontainers/sentieon:202308.01--h43eeafb_0' }" + 'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' : + 'biocontainers/sentieon:202308.02--h43eeafb_0' }" input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate From 5598939d0ef8206539a36518dc32a1a779c7420c Mon Sep 17 00:00:00 2001 From: asp8200 Date: Fri, 26 Apr 2024 17:18:40 +0000 Subject: [PATCH 18/72] Updating changelog --- CHANGELOG.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c9cd995156..101f278393 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1477](https://github.com/nf-core/sarek/pull/1477) - Back to dev - [#1482](https://github.com/nf-core/sarek/pull/1482) - Pin `nf-prov` plugin to `1.2.2` - [#1485](https://github.com/nf-core/sarek/pull/1485) - Update citation for publication +- [#1487](https://github.com/nf-core/sarek/pull/1487) - Update sentieon-modules to Sentieon `202308.02` ### Fixed @@ -23,6 +24,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Dependencies +| Dependency | Old version | New version | +| ---------- | ----------- | ----------- | +| sentieon | 202308.01 | 202308.02 | + ### Modules / Subworkflows ### Parameters From 944033a86a060e96cf34e0a22fcbd5b72a225aca Mon Sep 17 00:00:00 2001 From: asp8200 Date: Fri, 26 Apr 2024 17:24:00 +0000 Subject: [PATCH 19/72] Using monespace font for tools names in dependency table --- CHANGELOG.md | 44 ++++++++++++++++++++++---------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 101f278393..501fcc7b25 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,7 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Dependency | Old version | New version | | ---------- | ----------- | ----------- | -| sentieon | 202308.01 | 202308.02 | +| `sentieon` | 202308.01 | 202308.02 | ### Modules / Subworkflows @@ -98,16 +98,16 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe ### Dependencies -| Dependency | Old version | New version | -| ---------- | ----------- | ----------- | -| bcftools | 1.17 | 1.18 | -| ensemblvep | 110.0 | 111.0 | -| fgbio | 2.0.2 | 2.1.0 | -| gatk | 4.4.0.0 | 4.5.0.0 | -| gatk-spark | 4.4.0.0 | 4.5.0.0 | -| mosdepth | 0.3.3 | 0.3.6 | -| multiqc | 1.17 | 1.18 | -| samtools | 1.17 | 1.19.2 | +| Dependency | Old version | New version | +| ------------ | ----------- | ----------- | +| `bcftools` | 1.17 | 1.18 | +| `ensemblvep` | 110.0 | 111.0 | +| `fgbio` | 2.0.2 | 2.1.0 | +| `gatk` | 4.4.0.0 | 4.5.0.0 | +| `gatk-spark` | 4.4.0.0 | 4.5.0.0 | +| `mosdepth` | 0.3.3 | 0.3.6 | +| `multiqc` | 1.17 | 1.18 | +| `samtools` | 1.17 | 1.19.2 | ### Modules / Subworkflows @@ -116,9 +116,9 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe ### Parameter -| Old name | New name | -| -------------------------- | ------------------------ | -| bcftools_annotations_index | bcftools_annotations_tbi | +| Old name | New name | +| ---------------------------- | -------------------------- | +| `bcftools_annotations_index` | `bcftools_annotations_tbi` | ## [3.4.0](https://github.com/nf-core/sarek/releases/tag/3.4.0) - Pårtetjåkko @@ -168,8 +168,8 @@ Pårtetjåkko is a mountain in the south of the park. | Dependency | Old version | New version | | ---------- | ----------- | ----------- | -| fastqc | 0.11.9 | 0.12.1 | -| multiqc | 1.15 | 1.17 | +| `fastqc` | 0.11.9 | 0.12.1 | +| `multiqc` | 1.15 | 1.17 | ### Modules / Subworkflows @@ -202,9 +202,9 @@ Ráhpajávvre is the Lule Sámi spelling of Rapaselet. ### Dependencies -| Dependency | Old version | New version | -| -------------------------------- | ----------- | ----------- | -| Control-FREEC/assesssignificance | 11.6b | 11.6 | +| Dependency | Old version | New version | +| ---------------------------------- | ----------- | ----------- | +| `Control-FREEC/assesssignificance` | 11.6b | 11.6 | ## [3.3.1](https://github.com/nf-core/sarek/releases/tag/3.3.1) - Biellorippjávrre @@ -228,9 +228,9 @@ A lake near the Rapaselet delta. ### Dependencies -| Dependency | Old version | New version | -| ------------- | ----------- | ----------- | -| Control-FREEC | 11.6 | 11.6b | +| Dependency | Old version | New version | +| --------------- | ----------- | ----------- | +| `Control-FREEC` | 11.6 | 11.6b | ## [3.3.0](https://github.com/nf-core/sarek/releases/tag/3.3.0) - Rapaselet From 0aff681df465b40f2902eacf140538967d052be2 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Fri, 26 Apr 2024 17:25:30 +0000 Subject: [PATCH 20/72] More monospace font --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 501fcc7b25..b93d8aca8c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -347,7 +347,7 @@ Vuoinesluobbalah is a lake close to Bierikjávrre. ### Fixed -- [#1087](https://github.com/nf-core/sarek/pull/1087) - Fix wrong default memory in GATK4_CREATESEQUENCEDICTIONARY [#1085](https://github.com/nf-core/sarek/pull/1085) +- [#1087](https://github.com/nf-core/sarek/pull/1087) - Fix wrong default memory in `GATK4_CREATESEQUENCEDICTIONARY` [#1085](https://github.com/nf-core/sarek/pull/1085) - [#1089](https://github.com/nf-core/sarek/pull/1089) - Remove duplicated code - [#1093](https://github.com/nf-core/sarek/pull/1093) - Fixing Ascat by reverting meta.id in channels allele_files, loci_files, gc_file and rt_file to baseName - [#1098](https://github.com/nf-core/sarek/pull/1098) - Fix Channel issue in Mutect2 subworkflow [#1094](https://github.com/nf-core/sarek/pull/1094) From 020b33a9f69930551755cedce228b0e9f1429434 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 29 Apr 2024 05:45:25 +0000 Subject: [PATCH 21/72] Making sure certain channels are value channels --- main.nf | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/main.nf b/main.nf index 8b7940a558..93f896d6b9 100755 --- a/main.nf +++ b/main.nf @@ -177,12 +177,12 @@ workflow NFCORE_SAREK { rt_file = PREPARE_GENOME.out.rt_file // Tabix indexed vcf files - bcftools_annotations_tbi = params.bcftools_annotations ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi) : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.empty([]) - dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi) : PREPARE_GENOME.out.dbsnp_tbi : Channel.value([]) - germline_resource_tbi = params.germline_resource ? params.germline_resource_tbi ? Channel.fromPath(params.germline_resource_tbi) : PREPARE_GENOME.out.germline_resource_tbi : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries - known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : PREPARE_GENOME.out.known_indels_tbi : Channel.value([]) - known_snps_tbi = params.known_snps ? params.known_snps_tbi ? Channel.fromPath(params.known_snps_tbi) : PREPARE_GENOME.out.known_snps_tbi : Channel.value([]) - pon_tbi = params.pon ? params.pon_tbi ? Channel.fromPath(params.pon_tbi) : PREPARE_GENOME.out.pon_tbi : Channel.value([]) + bcftools_annotations_tbi = params.bcftools_annotations ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.empty([]) + dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : PREPARE_GENOME.out.dbsnp_tbi : Channel.value([]) + germline_resource_tbi = params.germline_resource ? params.germline_resource_tbi ? Channel.fromPath(params.germline_resource_tbi).collect() : PREPARE_GENOME.out.germline_resource_tbi : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries + known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : PREPARE_GENOME.out.known_indels_tbi : Channel.value([]) + known_snps_tbi = params.known_snps ? params.known_snps_tbi ? Channel.fromPath(params.known_snps_tbi).collect() : PREPARE_GENOME.out.known_snps_tbi : Channel.value([]) + pon_tbi = params.pon ? params.pon_tbi ? Channel.fromPath(params.pon_tbi).collect() : PREPARE_GENOME.out.pon_tbi : Channel.value([]) // known_sites is made by grouping both the dbsnp and the known snps/indels resources // Which can either or both be optional From eaa13736b69699670873e8aa45272fb5cd32ad6e Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 29 Apr 2024 06:03:48 +0000 Subject: [PATCH 22/72] Updating changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c9cd995156..1fb36a163f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed - [#1378](https://github.com/nf-core/sarek/pull/1378) - Improve cloud tests launch workflow to use matrix +- [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline` ### Removed From 956529fdee37f716af3db9e02f1f63cc52eb3dc9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 29 Apr 2024 11:50:14 +0200 Subject: [PATCH 23/72] add test data in igenomes --- conf/igenomes.config | 20 ++++++++++++++++++++ conf/test.config | 17 +++-------------- 2 files changed, 23 insertions(+), 14 deletions(-) diff --git a/conf/igenomes.config b/conf/igenomes.config index 5aa3e69805..a3f57e6d7e 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -320,5 +320,25 @@ params { fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" } + 'testdata.nf-core.sarek' { + dbsnp = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" + dbsnp_tbi = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" + dbsnp_vqsr = '--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz' + dict = "${params.igenomes_base}/genomics/homo_sapiens/genome/genome.dict" + fasta = "${params.igenomes_base}/genomics/homo_sapiens/genome/genome.fasta" + fasta_fai = "${params.igenomes_base}/genomics/homo_sapiens/genome/genome.fasta.fai" + germline_resource = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz" + germline_resource_tbi = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi" + intervals = "${params.igenomes_base}/genomics/homo_sapiens/genome/genome.interval_list" + known_indels = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" + known_indels_tbi = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi" + known_indels_vqsr = '--resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz' + ngscheckmate_bed = "${params.igenomes_base}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed" + snpeff_db = '105' + snpeff_genome = 'WBcel235' + vep_cache_version = '110' + vep_genome = 'WBcel235' + vep_species = 'caenorhabditis_elegans' + } } } diff --git a/conf/test.config b/conf/test.config index 0366015081..c2db191fc5 100644 --- a/conf/test.config +++ b/conf/test.config @@ -21,27 +21,16 @@ params { // Input data input = "${projectDir}/tests/csv/3.0/fastq_single.csv" - // No AWS iGenomes - genome = null - igenomes_ignore = true + // small genome on igenomes + igenomes_base = 's3://ngi-igenomes/testdata/nf-core/modules/' + genome = 'testdata.nf-core.sarek' // Small reference genome bcftools_annotations = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz" bcftools_annotations_tbi = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi" bcftools_header_lines = "${projectDir}/tests/config/bcfann_test_header.txt" - dbsnp = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" - fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta" - germline_resource = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz" - intervals = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.interval_list" - known_indels = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" - ngscheckmate_bed = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed" snpeff_cache = null - snpeff_db = '105' - snpeff_genome = 'WBcel235' vep_cache = null - vep_cache_version = '110' - vep_genome = 'WBcel235' - vep_species = 'caenorhabditis_elegans' // Sentieon sentieon_dnascope_model = "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model" From 2a37636206b952d5b78f5a78f9522c23cd081a2e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 29 Apr 2024 16:27:46 +0200 Subject: [PATCH 24/72] remove test_cache profile --- conf/test.config | 4 +- conf/test/cache.config | 133 ------------------ conf/test/targeted.config | 2 +- conf/test/tools.config | 16 ++- conf/test/tools_germline.config | 16 ++- conf/test/tools_somatic.config | 18 ++- conf/test/tools_somatic_ascat.config | 16 +-- conf/test/tools_tumoronly.config | 16 ++- conf/test/use_gatk_spark.config | 2 +- conf/test/variantcalling_channels.config | 7 +- tests/test_aligner_bwamem.yml | 4 +- tests/test_aligner_bwamem2.yml | 4 +- tests/test_aligner_dragmap.yml | 4 +- tests/test_alignment_to_fastq.yml | 2 +- tests/test_annotation_bcfann.yml | 2 +- tests/test_annotation_cache.yml | 6 +- tests/test_annotation_merge.yml | 4 +- tests/test_annotation_snpeff.yml | 2 +- tests/test_annotation_vep.yml | 4 +- tests/test_cnvkit.yml | 8 +- tests/test_concat_germline_vcfs.yml | 2 +- tests/test_controlfreec.yml | 6 +- tests/test_deepvariant.yml | 4 +- tests/test_fastp.yml | 4 +- tests/test_freebayes.yml | 12 +- tests/test_gatk4spark.yml | 6 +- tests/test_haplotypecaller.yml | 4 +- tests/test_haplotypecaller_skip_filter.yml | 4 +- tests/test_intervals.yml | 6 +- tests/test_joint_germline.yml | 6 +- tests/test_manta.yml | 12 +- tests/test_markduplicates_from_bam.yml | 4 +- tests/test_markduplicates_from_cram.yml | 4 +- tests/test_mpileup.yml | 8 +- tests/test_msisensorpro.yml | 4 +- tests/test_mutect2.yml | 4 +- tests/test_ngscheckmate.yml | 2 +- tests/test_prepare_recalibration_from_bam.yml | 4 +- .../test_prepare_recalibration_from_cram.yml | 4 +- tests/test_recalibrate_from_bam.yml | 4 +- tests/test_recalibrate_from_cram.yml | 4 +- tests/test_samplesheet_validation_spaces.yml | 2 +- tests/test_save_mapped.yml | 2 +- tests/test_save_output_as_bam_only.yml | 2 +- tests/test_sentieon_aligner_bwamem.yml | 8 +- tests/test_sentieon_dedup_from_bam.yml | 2 +- tests/test_sentieon_dedup_from_cram.yml | 2 +- tests/test_sentieon_dnascope.yml | 8 +- .../test_sentieon_dnascope_joint_germline.yml | 4 +- tests/test_sentieon_dnascope_skip_filter.yml | 4 +- tests/test_sentieon_haplotyper.yml | 10 +- ...est_sentieon_haplotyper_joint_germline.yml | 6 +- .../test_sentieon_haplotyper_skip_filter.yml | 4 +- tests/test_skip_all_qc.yml | 2 +- tests/test_skip_markduplicates.yml | 6 +- tests/test_strelka.yml | 14 +- tests/test_strelka_bp.yml | 4 +- tests/test_tiddit.yml | 6 +- tests/test_tools_manually.yml | 10 +- tests/test_tumor_normal_pair.yml | 2 +- tests/test_umi.yml | 6 +- 61 files changed, 188 insertions(+), 294 deletions(-) delete mode 100644 conf/test/cache.config diff --git a/conf/test.config b/conf/test.config index c2db191fc5..295b379b8e 100644 --- a/conf/test.config +++ b/conf/test.config @@ -26,8 +26,8 @@ params { genome = 'testdata.nf-core.sarek' // Small reference genome - bcftools_annotations = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz" - bcftools_annotations_tbi = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi" + bcftools_annotations = "${params.modules_testdata_base_path}/genomics/sarscov2/illumina/vcf/test2.vcf.gz" + bcftools_annotations_tbi = "${params.modules_testdata_base_path}/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi" bcftools_header_lines = "${projectDir}/tests/config/bcfann_test_header.txt" snpeff_cache = null vep_cache = null diff --git a/conf/test/cache.config b/conf/test/cache.config deleted file mode 100644 index 5e5145b6bc..0000000000 --- a/conf/test/cache.config +++ /dev/null @@ -1,133 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run nf-core/sarek -profile test,, --outdir -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -if (System.getenv('TEST_DATA_BASE')) { - if ("$TEST_DATA_BASE") { - params.test_data_base = "$TEST_DATA_BASE" - } -} - -try { - includeConfig "https://raw.githubusercontent.com/nf-core/modules/master/tests/config/test_data.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/modules test data config") -} - -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 = '6.5GB' - max_time = '8.h' - - // Input data - input = "${projectDir}/tests/csv/3.0/fastq_single.csv" - - // No AWS iGenomes - genome = null - igenomes_ignore = true - - // Small reference genome - bcftools_annotations = params.test_data['sarscov2']['illumina']['test2_vcf_gz'] - bcftools_annotations_tbi = params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'] - bcftools_header_lines = "${projectDir}/tests/config/bcfann_test_header.txt" - dbsnp = params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'] - fasta = params.test_data['homo_sapiens']['genome']['genome_fasta'] - germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'] - intervals = params.test_data['homo_sapiens']['genome']['genome_interval_list'] - known_indels = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'] - ngscheckmate_bed = params.test_data['homo_sapiens']['genome']['ngscheckmate_bed'] - snpeff_cache = null - snpeff_db = 105 - snpeff_genome = 'WBcel235' - vep_cache = null - vep_cache_version = 110 - vep_genome = 'WBcel235' - vep_species = 'caenorhabditis_elegans' - - // Sentieon - sentieon_dnascope_model = "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model" - - // default params - split_fastq = 0 // no FASTQ splitting - tools = 'strelka' // Variant calling with Strelka - - // Ignore params that will throw warning through params validation - validationSchemaIgnoreParams = 'genomes,test_data' -} - -process { - // This must contain .* in order to properly overwrite the standard config in test cases - withName:'.*:FREEC_SOMATIC'{ - ext.args = { - [ - "sample":[ - inputformat: "pileup", - mateorientation: "FR" - ], - "general":[ - bedgraphoutput: "TRUE", - noisydata: "TRUE", - minexpectedgc: "0", - readcountthreshold: "1", - sex: meta.sex, - window: "10", - ], - "control":[ - inputformat: "pileup", - mateorientation: "FR" - ] - ] - } - } - - withName: '.*:MUTECT2_PAIRED'{ - //sample name from when the test data was generated - ext.args = { "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample normal" } - } - - withName: '.*:FILTERVARIANTTRANCHES'{ - ext.args = { "--info-key CNN_1D --indel-tranche 0" } - } -} - -// Enable container engines/virtualisation envs for CI testing -// only works when specified with the profile ENV -// otherwise tests can be done with the regular provided profiles -if (System.getenv('PROFILE')) { - if ("$PROFILE" == "conda") { - conda.createTimeout = "120 min" - conda.enabled = true - charliecloud.enabled = false - docker.enabled = false - podman.enabled = false - shifter.enabled = false - singularity.enabled = false - } else if ("$PROFILE" == "docker") { - conda.enabled = false - docker.enabled = true - docker.runOptions = '-u $(id -u):$(id -g)' - charliecloud.enabled = false - podman.enabled = false - shifter.enabled = false - singularity.enabled = false - } else if ("$PROFILE" == "singularity") { - conda.enabled = false - singularity.autoMounts = true - singularity.enabled = true - charliecloud.enabled = false - docker.enabled = false - podman.enabled = false - shifter.enabled = false - } -} diff --git a/conf/test/targeted.config b/conf/test/targeted.config index 80fa1759d1..8ebbdf4392 100644 --- a/conf/test/targeted.config +++ b/conf/test/targeted.config @@ -10,7 +10,7 @@ */ params { - intervals = params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'] + intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/genome.multi_intervals.bed" nucleotides_per_second = 20 tools = null wes = true diff --git a/conf/test/tools.config b/conf/test/tools.config index a91389e27b..22e5c92d59 100644 --- a/conf/test/tools.config +++ b/conf/test/tools.config @@ -11,11 +11,17 @@ params { input = "${projectDir}/tests/csv/3.0/recalibrated.csv" - dbsnp = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'] - fasta = params.test_data['homo_sapiens']['genome']['genome_21_fasta'] - germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'] - intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'] - pon = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'] + genome = null + igenomes_ignore = true + dbsnp = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" + dbsnp_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" + fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" + fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + germline_resource = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" + germline_resource_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" + intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" + pon = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" + pon_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" nucleotides_per_second = 20 step = 'variant_calling' tools = null diff --git a/conf/test/tools_germline.config b/conf/test/tools_germline.config index 31cb79cd93..531f5e9b65 100644 --- a/conf/test/tools_germline.config +++ b/conf/test/tools_germline.config @@ -11,12 +11,18 @@ params { input = "${projectDir}/tests/csv/3.0/recalibrated_germline.csv" - dbsnp = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'] - fasta = params.test_data['homo_sapiens']['genome']['genome_21_fasta'] - intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'] - known_indels = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'] + genome = null + igenomes_ignore = true + dbsnp = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" + dbsnp_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" + fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" + fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" + known_indels = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" + known_indels_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" known_indels_vqsr = "--resource:1000G,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.hg38.vcf.gz" - known_snps = params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'] + known_snps = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz" + known_snps_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi" known_snps_vqsr = "--resource:hapmap,known=false,training=true,truth=true,prior=10.0 hapmap_3.3.hg38.vcf.gz" nucleotides_per_second = 20 step = 'variant_calling' diff --git a/conf/test/tools_somatic.config b/conf/test/tools_somatic.config index 93d4df8c19..6e040c81e8 100644 --- a/conf/test/tools_somatic.config +++ b/conf/test/tools_somatic.config @@ -11,12 +11,18 @@ params { input = "${projectDir}/tests/csv/3.0/recalibrated_somatic.csv" - chr_dir = params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'] - dbsnp = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'] - fasta = params.test_data['homo_sapiens']['genome']['genome_21_fasta'] - germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'] - intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'] - pon = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'] + genome = null + igenomes_ignore = true + chr_dir = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz" + dbsnp = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" + dbsnp_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" + fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" + fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + germline_resource = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" + germline_resource_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" + intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" + pon = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" + pon_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" nucleotides_per_second = 20 step = 'variant_calling' tools = null diff --git a/conf/test/tools_somatic_ascat.config b/conf/test/tools_somatic_ascat.config index 3f37bd4b3f..001d543726 100644 --- a/conf/test/tools_somatic_ascat.config +++ b/conf/test/tools_somatic_ascat.config @@ -10,14 +10,14 @@ */ params { - input = "${projectDir}/tests/csv/3.0/ascat_somatic.csv" - genome = 'GATK.GRCh37' - igenomes_ignore = false - ascat_loci = "G1000_loci_hg19.zip" - ascat_min_base_qual = 30 - chr_dir = params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'] - germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'] - intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'] + input = "${projectDir}/tests/csv/3.0/ascat_somatic.csv" + genome = 'GATK.GRCh37' + germline_resource_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" + ascat_loci = "G1000_loci_hg19.zip" + ascat_min_base_qual = 30 + chr_dir = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz" + germline_resource = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" + intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" step = 'variant_calling' tools = 'ascat' wes = false diff --git a/conf/test/tools_tumoronly.config b/conf/test/tools_tumoronly.config index b113fa76fd..72e87e6065 100644 --- a/conf/test/tools_tumoronly.config +++ b/conf/test/tools_tumoronly.config @@ -11,11 +11,17 @@ params { input = "${projectDir}/tests/csv/3.0/recalibrated_tumoronly.csv" - dbsnp = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'] - fasta = params.test_data['homo_sapiens']['genome']['genome_21_fasta'] - germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'] - intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'] - pon = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'] + genome = null + igenomes_ignore = true + dbsnp = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" + dbsnp_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" + fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" + fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + germline_resource = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" + germline_resource_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" + intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" + pon = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" + pon_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" nucleotides_per_second = 20 step = 'variant_calling' tools = null diff --git a/conf/test/use_gatk_spark.config b/conf/test/use_gatk_spark.config index bd40af1b77..43443d7e2a 100644 --- a/conf/test/use_gatk_spark.config +++ b/conf/test/use_gatk_spark.config @@ -10,7 +10,7 @@ */ params { + input = "${projectDir}/tests/csv/3.0/fastq_tumor_only.csv" tools = null use_gatk_spark = 'baserecalibrator,markduplicates' - input = "${projectDir}/tests/csv/3.0/fastq_tumor_only.csv" } diff --git a/conf/test/variantcalling_channels.config b/conf/test/variantcalling_channels.config index a6ff70387a..a83ce04ec9 100644 --- a/conf/test/variantcalling_channels.config +++ b/conf/test/variantcalling_channels.config @@ -11,8 +11,11 @@ params { input = "${projectDir}/tests/csv/3.0/recalibrated.csv" - fasta = params.test_data['homo_sapiens']['genome']['genome_21_fasta'] - intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'] + genome = null + igenomes_ignore = true + fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" + fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" nucleotides_per_second = 20 step = 'variant_calling' tools = null diff --git a/tests/test_aligner_bwamem.yml b/tests/test_aligner_bwamem.yml index ea51c0ccd5..fddd7d85df 100644 --- a/tests/test_aligner_bwamem.yml +++ b/tests/test_aligner_bwamem.yml @@ -1,5 +1,5 @@ - name: Run bwamem - command: nextflow run main.nf -profile test_cache --aligner bwa-mem --save_reference --outdir results + command: nextflow run main.nf -profile test --aligner bwa-mem --save_reference --outdir results tags: - aligner - bwamem @@ -74,7 +74,7 @@ - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - name: Build only index with bwa - command: nextflow run main.nf -profile test_cache --build_only_index --input false --outdir results + command: nextflow run main.nf -profile test --build_only_index --input false --outdir results tags: - aligner - build_only_index diff --git a/tests/test_aligner_bwamem2.yml b/tests/test_aligner_bwamem2.yml index 17760a558b..7c70129f35 100644 --- a/tests/test_aligner_bwamem2.yml +++ b/tests/test_aligner_bwamem2.yml @@ -1,5 +1,5 @@ - name: Run bwamem2 - command: nextflow run main.nf -profile test_cache --aligner bwa-mem2 --save_reference --outdir results + command: nextflow run main.nf -profile test --aligner bwa-mem2 --save_reference --outdir results tags: - aligner - bwamem2 @@ -74,7 +74,7 @@ - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - name: Build only index with bwa-mem2 - command: nextflow run main.nf -profile test_cache --build_only_index --aligner bwa-mem2 --input false --outdir results + command: nextflow run main.nf -profile test --build_only_index --aligner bwa-mem2 --input false --outdir results tags: - aligner - build_only_index diff --git a/tests/test_aligner_dragmap.yml b/tests/test_aligner_dragmap.yml index a4960d8e02..1b4349b80d 100644 --- a/tests/test_aligner_dragmap.yml +++ b/tests/test_aligner_dragmap.yml @@ -1,5 +1,5 @@ - name: Run dragmap - command: nextflow run main.nf -profile test_cache --aligner dragmap --save_reference --outdir results + command: nextflow run main.nf -profile test --aligner dragmap --save_reference --outdir results tags: - aligner - dragmap @@ -87,7 +87,7 @@ - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - name: Build only index with dragmap - command: nextflow run main.nf -profile test_cache --build_only_index --aligner dragmap --input false --outdir results + command: nextflow run main.nf -profile test --build_only_index --aligner dragmap --input false --outdir results tags: - aligner - build_only_index diff --git a/tests/test_alignment_to_fastq.yml b/tests/test_alignment_to_fastq.yml index 6077b745d4..1b64f422e8 100644 --- a/tests/test_alignment_to_fastq.yml +++ b/tests/test_alignment_to_fastq.yml @@ -1,5 +1,5 @@ - name: Run alignment to fastq and then remap on bam files - command: nextflow run main.nf -profile test_cache,alignment_to_fastq --outdir results + command: nextflow run main.nf -profile test,alignment_to_fastq --outdir results tags: - alignment_to_fastq - input_bam diff --git a/tests/test_annotation_bcfann.yml b/tests/test_annotation_bcfann.yml index 5b9546b961..99ac781d8e 100644 --- a/tests/test_annotation_bcfann.yml +++ b/tests/test_annotation_bcfann.yml @@ -1,5 +1,5 @@ - name: Run bcfann - command: nextflow run main.nf -profile test_cache,annotation --tools bcfann --outdir results + command: nextflow run main.nf -profile test,annotation --tools bcfann --outdir results tags: - annotation - bcfann diff --git a/tests/test_annotation_cache.yml b/tests/test_annotation_cache.yml index fd84fb47e4..290169d32d 100644 --- a/tests/test_annotation_cache.yml +++ b/tests/test_annotation_cache.yml @@ -1,5 +1,5 @@ - name: Only download annotation cache - command: nextflow run main.nf -profile test_cache,annotation --tools merge --download_cache --input false --build_only_index --outdir results + command: nextflow run main.nf -profile test,annotation --tools merge --download_cache --input false --build_only_index --outdir results tags: - annotation - cache @@ -13,7 +13,7 @@ should_exist: false - name: Fail to locate VEP cache - command: nextflow run main.nf -profile test_cache,annotation --vep_cache s3://annotation-cache/vep_cache/ --vep_cache_version 1 --tools vep --input false --build_only_index --outdir results + command: nextflow run main.nf -profile test,annotation --vep_cache s3://annotation-cache/vep_cache/ --vep_cache_version 1 --tools vep --input false --build_only_index --outdir results tags: - annotation - cache @@ -21,7 +21,7 @@ exit_code: 1 - name: Fail to locate snpEff cache - command: nextflow run main.nf -profile test_cache,annotation --snpeff_cache s3://annotation-cache/snpeff_cache/ --snpeff_genome na --tools snpeff --input false --build_only_index --outdir results + command: nextflow run main.nf -profile test,annotation --snpeff_cache s3://annotation-cache/snpeff_cache/ --snpeff_genome na --tools snpeff --input false --build_only_index --outdir results tags: - annotation - cache diff --git a/tests/test_annotation_merge.yml b/tests/test_annotation_merge.yml index 21351f1cfc..7c39948743 100644 --- a/tests/test_annotation_merge.yml +++ b/tests/test_annotation_merge.yml @@ -1,5 +1,5 @@ - name: Run snpEff followed by VEP - command: nextflow run main.nf -profile test_cache,annotation --tools merge --outdir results --download_cache + command: nextflow run main.nf -profile test,annotation --tools merge --outdir results --download_cache tags: - annotation - merge @@ -28,7 +28,7 @@ - path: results/reports/EnsemblVEP/test/test_VEP.ann.summary.html should_exist: false - name: Run VEP and snpEff followed by VEP - command: nextflow run main.nf -profile test_cache,annotation --tools merge,snpeff,vep --outdir results --download_cache + command: nextflow run main.nf -profile test,annotation --tools merge,snpeff,vep --outdir results --download_cache tags: - annotation - merge diff --git a/tests/test_annotation_snpeff.yml b/tests/test_annotation_snpeff.yml index d6ce2ee48d..5ad71d0664 100644 --- a/tests/test_annotation_snpeff.yml +++ b/tests/test_annotation_snpeff.yml @@ -1,5 +1,5 @@ - name: Run snpEff - command: nextflow run main.nf -profile test_cache,annotation --tools snpeff --outdir results --download_cache + command: nextflow run main.nf -profile test,annotation --tools snpeff --outdir results --download_cache tags: - annotation - snpeff diff --git a/tests/test_annotation_vep.yml b/tests/test_annotation_vep.yml index 176c85020c..c8c16747b2 100644 --- a/tests/test_annotation_vep.yml +++ b/tests/test_annotation_vep.yml @@ -1,5 +1,5 @@ - name: Run VEP - command: nextflow run main.nf -profile test_cache,annotation --tools vep --outdir results --download_cache + command: nextflow run main.nf -profile test,annotation --tools vep --outdir results --download_cache tags: - annotation - vep @@ -12,7 +12,7 @@ - path: results/reports/EnsemblVEP/test/test_VEP.ann.summary.html contains: ["test.vcf.gzOutput filetest_VEP.ann.vcf.gz"] - name: Run VEP with fasta - command: nextflow run main.nf -profile test_cache,annotation --tools vep --vep_include_fasta --outdir results --download_cache + command: nextflow run main.nf -profile test,annotation --tools vep --vep_include_fasta --outdir results --download_cache tags: - annotation - vep diff --git a/tests/test_cnvkit.yml b/tests/test_cnvkit.yml index 8e9017c70b..87adbc33c6 100644 --- a/tests/test_cnvkit.yml +++ b/tests/test_cnvkit.yml @@ -1,5 +1,5 @@ - name: Run variant calling on somatic samples with cnvkit - command: nextflow run main.nf -profile test_cache,tools_somatic --tools cnvkit --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools cnvkit --outdir results tags: - cnvkit - copy_number_calling @@ -82,7 +82,7 @@ - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on tumor_only sample with cnvkit - command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools cnvkit --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --tools cnvkit --outdir results tags: - cnvkit - copy_number_calling @@ -124,7 +124,7 @@ md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on germline sample with cnvkit - command: nextflow run main.nf -profile test_cache,tools_germline --tools cnvkit --outdir results + command: nextflow run main.nf -profile test,tools_germline --tools cnvkit --outdir results tags: - cnvkit - copy_number_calling @@ -168,7 +168,7 @@ md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal - command: nextflow run main.nf -profile test_cache,tools_somatic --tools cnvkit --only_paired_variant_calling --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools cnvkit --only_paired_variant_calling --outdir results tags: - cnvkit - somatic diff --git a/tests/test_concat_germline_vcfs.yml b/tests/test_concat_germline_vcfs.yml index 8a32231ac8..97a2453fbc 100644 --- a/tests/test_concat_germline_vcfs.yml +++ b/tests/test_concat_germline_vcfs.yml @@ -1,5 +1,5 @@ - name: Run all germline variant callers and check for existence of concatenated vcf-files - command: nextflow run main.nf -profile test_cache --input ./tests/csv/3.0/mapped_joint_bam.csv --concatenate_vcfs --tools deepvariant,freebayes,haplotypecaller,manta,mpileup,strelka,tiddit --step variant_calling --outdir results + command: nextflow run main.nf -profile test --input ./tests/csv/3.0/mapped_joint_bam.csv --concatenate_vcfs --tools deepvariant,freebayes,haplotypecaller,manta,mpileup,strelka,tiddit --step variant_calling --outdir results tags: - concatenate_vcfs files: diff --git a/tests/test_controlfreec.yml b/tests/test_controlfreec.yml index 4d938351f4..c3353561a0 100644 --- a/tests/test_controlfreec.yml +++ b/tests/test_controlfreec.yml @@ -1,5 +1,5 @@ - name: Run variant calling on somatic samples with controlfreec - command: nextflow run main.nf -profile test_cache,tools_somatic --tools controlfreec --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools controlfreec --outdir results tags: - controlfreec - somatic @@ -75,7 +75,7 @@ - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic samples with controlfreec without intervals - command: nextflow run main.nf -profile test_cache,tools_somatic --tools controlfreec --no_intervals -stub-run --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools controlfreec --no_intervals -stub-run --outdir results tags: - controlfreec - no_intervals @@ -147,7 +147,7 @@ - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on tumor_only sample with controlfreec - command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools controlfreec -stub-run --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --tools controlfreec -stub-run --outdir results tags: - controlfreec - tumor_only diff --git a/tests/test_deepvariant.yml b/tests/test_deepvariant.yml index cead54aa47..42660bd78a 100644 --- a/tests/test_deepvariant.yml +++ b/tests/test_deepvariant.yml @@ -1,5 +1,5 @@ - name: Run variant calling on germline sample with deepvariant - command: nextflow run main.nf -profile test_cache,tools_germline --tools deepvariant --outdir results + command: nextflow run main.nf -profile test,tools_germline --tools deepvariant --outdir results tags: - deepvariant - germline @@ -36,7 +36,7 @@ md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on germline sample with deepvariant without intervals - command: nextflow run main.nf -profile test_cache,tools_germline --tools deepvariant --no_intervals --outdir results + command: nextflow run main.nf -profile test,tools_germline --tools deepvariant --no_intervals --outdir results tags: - deepvariant - germline diff --git a/tests/test_fastp.yml b/tests/test_fastp.yml index 7ea4dc4bd7..e8fe306468 100644 --- a/tests/test_fastp.yml +++ b/tests/test_fastp.yml @@ -1,5 +1,5 @@ - name: Run trimming pipeline - command: nextflow run main.nf -profile test_cache,trimming --save_trimmed --outdir results + command: nextflow run main.nf -profile test,trimming --save_trimmed --outdir results tags: - fastp - preprocessing @@ -55,7 +55,7 @@ - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - name: Run split fastq module - command: nextflow run main.nf -profile test_cache,split_fastq --outdir results + command: nextflow run main.nf -profile test,split_fastq --outdir results tags: - fastp - preprocessing diff --git a/tests/test_freebayes.yml b/tests/test_freebayes.yml index bd76fa1411..6809ac0b4e 100644 --- a/tests/test_freebayes.yml +++ b/tests/test_freebayes.yml @@ -1,5 +1,5 @@ - name: Run variant calling on germline sample with freebayes - command: nextflow run main.nf -profile test_cache,targeted --tools freebayes --outdir results + command: nextflow run main.nf -profile test,targeted --tools freebayes --outdir results tags: - freebayes - germline @@ -73,7 +73,7 @@ - path: results/freebayes should_exist: false - name: Run variant calling on germline sample with freebayes without intervals - command: nextflow run main.nf -profile test_cache --tools freebayes --no_intervals --outdir results + command: nextflow run main.nf -profile test --tools freebayes --no_intervals --outdir results tags: - freebayes - germline @@ -146,7 +146,7 @@ - path: results/freebayes should_exist: false - name: Run variant calling on somatic sample with freebayes - command: nextflow run main.nf -profile test_cache,pair,targeted --tools freebayes --outdir results + command: nextflow run main.nf -profile test,pair,targeted --tools freebayes --outdir results tags: - freebayes - somatic @@ -276,7 +276,7 @@ - path: results/freebayes should_exist: false - name: Run variant calling on somatic sample with freebayes without intervals - command: nextflow run main.nf -profile test_cache,pair,targeted --tools freebayes --no_intervals --outdir results + command: nextflow run main.nf -profile test,pair,targeted --tools freebayes --no_intervals --outdir results tags: - freebayes - somatic @@ -389,7 +389,7 @@ - path: results/freebayes should_exist: false - name: Run variant calling on tumor_only sample with freebayes - command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools freebayes --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes --outdir results tags: - freebayes - tumor_only @@ -413,7 +413,7 @@ - path: results/freebayes should_exist: false - name: Run variant calling on tumor_only sample with freebayes without intervals - command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools freebayes --no_intervals --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes --no_intervals --outdir results tags: - freebayes - no_intervals diff --git a/tests/test_gatk4spark.yml b/tests/test_gatk4spark.yml index 6462bd130a..270bbdd775 100644 --- a/tests/test_gatk4spark.yml +++ b/tests/test_gatk4spark.yml @@ -1,5 +1,5 @@ - name: Run default pipeline with gatk4spark - command: nextflow run main.nf -profile test_cache,use_gatk_spark,spark --outdir results + command: nextflow run main.nf -profile test,use_gatk_spark,spark --outdir results tags: - gatk4spark - preprocessing @@ -49,7 +49,7 @@ - path: results/preprocessing/mapped/ should_exist: false - name: Run default pipeline with gatk4spark and skipping all QC steps - command: nextflow run main.nf -profile test_cache,use_gatk_spark,spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results + command: nextflow run main.nf -profile test,use_gatk_spark,spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results tags: - gatk4spark - preprocessing @@ -82,7 +82,7 @@ - path: results/reports/samtools should_exist: false - name: Run save_output_as_bam with gatk4 spark - command: nextflow run main.nf -profile test_cache,use_gatk_spark,spark --save_output_as_bam --outdir results + command: nextflow run main.nf -profile test,use_gatk_spark,spark --save_output_as_bam --outdir results tags: - gatk4spark - preprocessing diff --git a/tests/test_haplotypecaller.yml b/tests/test_haplotypecaller.yml index 2f76698774..937198c429 100644 --- a/tests/test_haplotypecaller.yml +++ b/tests/test_haplotypecaller.yml @@ -1,5 +1,5 @@ - name: Run variant calling on germline sample with haplotypecaller - command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --outdir results + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --outdir results tags: - germline - haplotypecaller @@ -47,7 +47,7 @@ - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with haplotypecaller without intervals - command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --no_intervals --outdir results + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --no_intervals --outdir results tags: - germline - haplotypecaller diff --git a/tests/test_haplotypecaller_skip_filter.yml b/tests/test_haplotypecaller_skip_filter.yml index 9b68f220e6..5741547e4f 100644 --- a/tests/test_haplotypecaller_skip_filter.yml +++ b/tests/test_haplotypecaller_skip_filter.yml @@ -1,5 +1,5 @@ - name: Run variant calling on germline sample with haplotypecaller and skip filter - command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --skip_tools haplotypecaller_filter --outdir results + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --skip_tools haplotypecaller_filter --outdir results tags: - germline - haplotypecaller_skip_filter @@ -50,7 +50,7 @@ md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with haplotypecaller without intervals and skip filter - command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --skip_tools haplotypecaller_filter --no_intervals --outdir results + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --skip_tools haplotypecaller_filter --no_intervals --outdir results tags: - germline - haplotypecaller_skip_filter diff --git a/tests/test_intervals.yml b/tests/test_intervals.yml index 0196376807..df0abfdfa0 100644 --- a/tests/test_intervals.yml +++ b/tests/test_intervals.yml @@ -1,5 +1,5 @@ - name: Run default pipeline with target bed - command: nextflow run main.nf -profile test_cache,targeted --outdir results + command: nextflow run main.nf -profile test,targeted --outdir results tags: - intervals - preprocessing @@ -58,7 +58,7 @@ - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - name: Run pipeline with intervals false - command: nextflow run main.nf -profile test_cache --intervals false --save_reference --outdir results + command: nextflow run main.nf -profile test --intervals false --save_reference --outdir results tags: - intervals - intervals_false @@ -109,7 +109,7 @@ - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - name: Run default pipeline without intervals - command: nextflow run main.nf -profile test_cache,no_intervals --outdir results + command: nextflow run main.nf -profile test,no_intervals --outdir results tags: - intervals - no_intervals diff --git a/tests/test_joint_germline.yml b/tests/test_joint_germline.yml index e01a7ea1a3..8379820f42 100644 --- a/tests/test_joint_germline.yml +++ b/tests/test_joint_germline.yml @@ -1,5 +1,5 @@ - name: Run joint germline variant calling with haplotypecaller - command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --known_snps_vqsr false --known_indels_vqsr false + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --known_snps_vqsr false --known_indels_vqsr false tags: - germline - joint_germline @@ -53,7 +53,7 @@ md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with haplotypecaller all intervals at once - command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --nucleotides_per_second 100 + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --nucleotides_per_second 100 tags: - germline - joint_germline @@ -107,7 +107,7 @@ md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with haplotypecaller with Stub for VQSR - command: nextflow run main.nf -profile test_cache,tools_germline --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results -stub-run + command: nextflow run main.nf -profile test,tools_germline --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results -stub-run tags: - germline - joint_germline diff --git a/tests/test_manta.yml b/tests/test_manta.yml index b119ca80b7..2d4fefe378 100644 --- a/tests/test_manta.yml +++ b/tests/test_manta.yml @@ -1,5 +1,5 @@ - name: Run variant calling on germline sample with manta - command: nextflow run main.nf -profile test_cache,tools_germline --tools manta --outdir results + command: nextflow run main.nf -profile test,tools_germline --tools manta --outdir results tags: - germline - manta @@ -34,7 +34,7 @@ md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on germline sample with manta without intervals - command: nextflow run main.nf -profile test_cache,tools_germline --tools manta --no_intervals --outdir results + command: nextflow run main.nf -profile test,tools_germline --tools manta --no_intervals --outdir results tags: - germline - manta @@ -74,7 +74,7 @@ md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on tumor_only sample with manta - command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools manta --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --tools manta --outdir results tags: - manta - tumor_only @@ -109,7 +109,7 @@ md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on tumor_only sample with manta without intervals - command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools manta --no_intervals --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --tools manta --no_intervals --outdir results tags: - manta - no_intervals @@ -149,7 +149,7 @@ md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on somatic sample with manta - command: nextflow run main.nf -profile test_cache,tools_somatic --tools manta --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools manta --outdir results tags: - manta - somatic @@ -221,7 +221,7 @@ - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with manta without intervals - command: nextflow run main.nf -profile test_cache,tools_somatic --tools manta --no_intervals --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools manta --no_intervals --outdir results tags: - manta - no_intervals diff --git a/tests/test_markduplicates_from_bam.yml b/tests/test_markduplicates_from_bam.yml index d6191216bd..caca7ccc46 100644 --- a/tests/test_markduplicates_from_bam.yml +++ b/tests/test_markduplicates_from_bam.yml @@ -1,5 +1,5 @@ - name: Run markduplicates starting from BAM - command: nextflow run main.nf -profile test_cache,markduplicates_bam --outdir results + command: nextflow run main.nf -profile test,markduplicates_bam --outdir results tags: - input_bam - gatk4/markduplicates @@ -50,7 +50,7 @@ # conda changes md5sums for test - name: Run skip markduplicates bam from step markduplicates - command: nextflow run main.nf -profile test_cache,markduplicates_bam,skip_markduplicates --outdir results + command: nextflow run main.nf -profile test,markduplicates_bam,skip_markduplicates --outdir results tags: - input_bam - markduplicates diff --git a/tests/test_markduplicates_from_cram.yml b/tests/test_markduplicates_from_cram.yml index f36619f719..b101148aa8 100644 --- a/tests/test_markduplicates_from_cram.yml +++ b/tests/test_markduplicates_from_cram.yml @@ -1,5 +1,5 @@ - name: Run markduplicates starting from CRAM - command: nextflow run main.nf -profile test_cache,markduplicates_cram --outdir results + command: nextflow run main.nf -profile test,markduplicates_cram --outdir results tags: - input_cram - gatk4/markduplicates @@ -51,7 +51,7 @@ - path: results/preprocessing/mapped/ should_exist: false - name: Run skip markduplicates cram from step markduplicates - command: nextflow run main.nf -profile test_cache,markduplicates_cram,skip_markduplicates --outdir results + command: nextflow run main.nf -profile test,markduplicates_cram,skip_markduplicates --outdir results tags: - input_cram - markduplicates diff --git a/tests/test_mpileup.yml b/tests/test_mpileup.yml index f7c5d87749..25fefd0eb0 100644 --- a/tests/test_mpileup.yml +++ b/tests/test_mpileup.yml @@ -1,5 +1,5 @@ - name: Run variant calling on tumor_only sample to test mpileup - command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools mpileup --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --tools mpileup --outdir results tags: - tumor_only - mpileup @@ -25,7 +25,7 @@ md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on tumor_only sample to test mpileup without intervals - command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools mpileup --no_intervals --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --tools mpileup --no_intervals --outdir results tags: - tumor_only - mpileup @@ -56,7 +56,7 @@ md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on germline sample to test mpileup - command: nextflow run main.nf -profile test_cache,tools_germline --tools mpileup --outdir results + command: nextflow run main.nf -profile test,tools_germline --tools mpileup --outdir results tags: - germline - mpileup @@ -82,7 +82,7 @@ md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on germline sample to test mpileup without intervals - command: nextflow run main.nf -profile test_cache,tools_germline --tools mpileup --no_intervals --outdir results + command: nextflow run main.nf -profile test,tools_germline --tools mpileup --no_intervals --outdir results tags: - germline - mpileup diff --git a/tests/test_msisensorpro.yml b/tests/test_msisensorpro.yml index 173dbcf5ca..47962d5fa0 100644 --- a/tests/test_msisensorpro.yml +++ b/tests/test_msisensorpro.yml @@ -1,5 +1,5 @@ - name: Run variant calling on somatic sample with msisensor-pro - command: nextflow run main.nf -profile test_cache,tools_somatic --tools msisensorpro --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools msisensorpro --outdir results tags: - msisensorpro - somatic @@ -37,7 +37,7 @@ - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Build only index with msisensorpro - command: nextflow run main.nf -profile test_cache --build_only_index --tools msisensorpro --input false --outdir results + command: nextflow run main.nf -profile test --build_only_index --tools msisensorpro --input false --outdir results tags: - build_only_index - msisensorpro diff --git a/tests/test_mutect2.yml b/tests/test_mutect2.yml index 52b422b1bf..28d9f5f933 100644 --- a/tests/test_mutect2.yml +++ b/tests/test_mutect2.yml @@ -1,5 +1,5 @@ - name: Run variant calling on tumor only sample with mutect2 - command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools mutect2 --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --tools mutect2 --outdir results tags: - mutect2 - tumor_only @@ -50,7 +50,7 @@ md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on tumor only sample with mutect2 without intervals - command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools mutect2 --no_intervals --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --tools mutect2 --no_intervals --outdir results tags: - mutect2 - no_intervals diff --git a/tests/test_ngscheckmate.yml b/tests/test_ngscheckmate.yml index 8923ddc9ec..b48a62b629 100644 --- a/tests/test_ngscheckmate.yml +++ b/tests/test_ngscheckmate.yml @@ -1,5 +1,5 @@ - name: Check ngscheckmate is working - command: nextflow run main.nf -profile test_cache,tools --tools ngscheckmate --outdir results + command: nextflow run main.nf -profile test,tools --tools ngscheckmate --outdir results tags: - ngscheckmate - tools diff --git a/tests/test_prepare_recalibration_from_bam.yml b/tests/test_prepare_recalibration_from_bam.yml index 3d2560058c..b5ab788e78 100644 --- a/tests/test_prepare_recalibration_from_bam.yml +++ b/tests/test_prepare_recalibration_from_bam.yml @@ -1,5 +1,5 @@ - name: Run prepare_recalibration starting from bam - command: nextflow run main.nf -profile test_cache,prepare_recalibration_bam --outdir results + command: nextflow run main.nf -profile test,prepare_recalibration_bam --outdir results tags: - input_bam - prepare_recalibration @@ -37,7 +37,7 @@ - path: results/preprocessing/markduplicates/ should_exist: false - name: Run prepare_recalibration starting from bam and skip baserecalibration - command: nextflow run main.nf -profile test_cache,prepare_recalibration_bam,skip_bqsr --tools strelka --outdir results + command: nextflow run main.nf -profile test,prepare_recalibration_bam,skip_bqsr --tools strelka --outdir results tags: - input_bam - prepare_recalibration diff --git a/tests/test_prepare_recalibration_from_cram.yml b/tests/test_prepare_recalibration_from_cram.yml index d69fa91525..d207c6f190 100644 --- a/tests/test_prepare_recalibration_from_cram.yml +++ b/tests/test_prepare_recalibration_from_cram.yml @@ -1,5 +1,5 @@ - name: Run prepare_recalibration starting from cram - command: nextflow run main.nf -profile test_cache,prepare_recalibration_cram --outdir results + command: nextflow run main.nf -profile test,prepare_recalibration_cram --outdir results tags: - input_cram - prepare_recalibration @@ -31,7 +31,7 @@ - path: results/preprocessing/markduplicates/ should_exist: false - name: Run prepare_recalibration starting from cram and skip baserecalibration - command: nextflow run main.nf -profile test_cache,prepare_recalibration_cram,skip_bqsr --tools strelka --outdir results + command: nextflow run main.nf -profile test,prepare_recalibration_cram,skip_bqsr --tools strelka --outdir results tags: - input_cram - prepare_recalibration diff --git a/tests/test_recalibrate_from_bam.yml b/tests/test_recalibrate_from_bam.yml index cc1a3e114a..41d0c91e4a 100644 --- a/tests/test_recalibrate_from_bam.yml +++ b/tests/test_recalibrate_from_bam.yml @@ -1,5 +1,5 @@ - name: Run Recalibration starting from bam - command: nextflow run main.nf -profile test_cache,recalibrate_bam --outdir results + command: nextflow run main.nf -profile test,recalibrate_bam --outdir results tags: - input_bam - recalibrate @@ -33,7 +33,7 @@ - path: results/preprocessing/markduplicates/ should_exist: false - name: Run Recalibration starting from bam and skip baserecalibration - command: nextflow run main.nf -profile test_cache,recalibrate_bam,skip_bqsr --tools strelka --outdir results + command: nextflow run main.nf -profile test,recalibrate_bam,skip_bqsr --tools strelka --outdir results tags: - input_bam - recalibrate diff --git a/tests/test_recalibrate_from_cram.yml b/tests/test_recalibrate_from_cram.yml index e843424f50..5f5d0badd3 100644 --- a/tests/test_recalibrate_from_cram.yml +++ b/tests/test_recalibrate_from_cram.yml @@ -1,5 +1,5 @@ - name: Run Recalibration starting from cram - command: nextflow run main.nf -profile test_cache,recalibrate_cram --outdir results + command: nextflow run main.nf -profile test,recalibrate_cram --outdir results tags: - input_cram - recalibrate @@ -29,7 +29,7 @@ - path: results/preprocessing/markduplicates/ should_exist: false - name: Run Recalibration starting from cram and skip baserecalibration - command: nextflow run main.nf -profile test_cache,recalibrate_cram,skip_bqsr --tools strelka --outdir results + command: nextflow run main.nf -profile test,recalibrate_cram,skip_bqsr --tools strelka --outdir results tags: - input_cram - recalibrate diff --git a/tests/test_samplesheet_validation_spaces.yml b/tests/test_samplesheet_validation_spaces.yml index edd0576d3a..f0983b0518 100644 --- a/tests/test_samplesheet_validation_spaces.yml +++ b/tests/test_samplesheet_validation_spaces.yml @@ -1,5 +1,5 @@ - name: Test that pipeline fail when sample/patient name contain space - command: nextflow run main.nf -profile test_cache --input ./tests/csv/3.0/sample_with_space.csv --outdir results + command: nextflow run main.nf -profile test --input ./tests/csv/3.0/sample_with_space.csv --outdir results tags: - sample_with_space - validation_checks diff --git a/tests/test_save_mapped.yml b/tests/test_save_mapped.yml index 7868da9d35..0446ec902f 100644 --- a/tests/test_save_mapped.yml +++ b/tests/test_save_mapped.yml @@ -1,5 +1,5 @@ - name: Run save_mapped - command: nextflow run main.nf -profile test_cache --save_mapped --outdir results + command: nextflow run main.nf -profile test --save_mapped --outdir results tags: - default_extended - preprocessing diff --git a/tests/test_save_output_as_bam_only.yml b/tests/test_save_output_as_bam_only.yml index bc577c0ae8..08f67d44f4 100644 --- a/tests/test_save_output_as_bam_only.yml +++ b/tests/test_save_output_as_bam_only.yml @@ -1,5 +1,5 @@ - name: Run save_output_as_bam - command: nextflow run main.nf -profile test_cache --save_output_as_bam --outdir results + command: nextflow run main.nf -profile test --save_output_as_bam --outdir results tags: - default_extended - preprocessing diff --git a/tests/test_sentieon_aligner_bwamem.yml b/tests/test_sentieon_aligner_bwamem.yml index 37f883312d..6bf048cecb 100644 --- a/tests/test_sentieon_aligner_bwamem.yml +++ b/tests/test_sentieon_aligner_bwamem.yml @@ -1,5 +1,5 @@ - name: Run sentieon bwamem - command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --save_reference --outdir results + command: nextflow run main.nf -profile test,software_license --sentieon_extension --aligner sentieon-bwamem --save_reference --outdir results tags: - aligner - sentieon/bwamem @@ -74,7 +74,7 @@ - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - name: Build only index with sentieon bwa - command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --build_only_index --outdir results + command: nextflow run main.nf -profile test,software_license --sentieon_extension --aligner sentieon-bwamem --build_only_index --outdir results tags: - aligner - build_only_index @@ -106,7 +106,7 @@ - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi # conda changes md5sums for test - name: Run sentieon bwamem save bam - command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --save_mapped --save_output_as_bam --outdir results + command: nextflow run main.nf -profile test,software_license --sentieon_extension --aligner sentieon-bwamem --save_mapped --save_output_as_bam --outdir results tags: - aligner - sentieon/bwamem @@ -160,7 +160,7 @@ - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - name: Run sentieon bwamem save cram - command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --save_mapped --outdir results + command: nextflow run main.nf -profile test,software_license --sentieon_extension --aligner sentieon-bwamem --save_mapped --outdir results tags: - aligner - sentieon/bwamem diff --git a/tests/test_sentieon_dedup_from_bam.yml b/tests/test_sentieon_dedup_from_bam.yml index 54df60e415..306ae5634f 100644 --- a/tests/test_sentieon_dedup_from_bam.yml +++ b/tests/test_sentieon_dedup_from_bam.yml @@ -1,5 +1,5 @@ - name: Run sentieon dedup starting from BAM - command: nextflow run main.nf -profile test_cache,software_license,sentieon_dedup_bam --sentieon_extension --outdir results + command: nextflow run main.nf -profile test,software_license,sentieon_dedup_bam --sentieon_extension --outdir results tags: - input_bam - preprocessing diff --git a/tests/test_sentieon_dedup_from_cram.yml b/tests/test_sentieon_dedup_from_cram.yml index 87dfdebfa7..abf6f57da6 100644 --- a/tests/test_sentieon_dedup_from_cram.yml +++ b/tests/test_sentieon_dedup_from_cram.yml @@ -1,5 +1,5 @@ - name: Run sentieon dedup starting from CRAM - command: nextflow run main.nf -profile test_cache,software_license,sentieon_dedup_cram --sentieon_extension --outdir results + command: nextflow run main.nf -profile test,software_license,sentieon_dedup_cram --sentieon_extension --outdir results tags: - input_cram - preprocessing diff --git a/tests/test_sentieon_dnascope.yml b/tests/test_sentieon_dnascope.yml index 49b88ca43c..889954b90e 100644 --- a/tests/test_sentieon_dnascope.yml +++ b/tests/test_sentieon_dnascope.yml @@ -1,5 +1,5 @@ - name: Run variant calling on germline sample with sentieons dnascope - command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results + command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results tags: - germline - sentieon/dnascope @@ -45,7 +45,7 @@ md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons dnascope without intervals - command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --no_intervals --outdir results + command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --no_intervals --outdir results tags: - germline - sentieon/dnascope @@ -97,7 +97,7 @@ - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons dnascope output gvcf - command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode gvcf + command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode gvcf tags: - germline - sentieon/dnascope @@ -146,7 +146,7 @@ md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons dnascope output both gvcf and vcf - command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode variant,gvcf + command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode variant,gvcf tags: - germline - sentieon/dnascope diff --git a/tests/test_sentieon_dnascope_joint_germline.yml b/tests/test_sentieon_dnascope_joint_germline.yml index d5775cc048..84a217eefe 100644 --- a/tests/test_sentieon_dnascope_joint_germline.yml +++ b/tests/test_sentieon_dnascope_joint_germline.yml @@ -1,5 +1,5 @@ - name: Run joint germline variant calling with sentieon dnascope - command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_dnascope --step variant_calling --joint_germline --outdir results --sentieon_dnascope_emit_mode gvcf + command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_dnascope --step variant_calling --joint_germline --outdir results --sentieon_dnascope_emit_mode gvcf tags: - germline - sentieon/dnascope_joint_germline @@ -51,7 +51,7 @@ - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with sentieon dnascope all intervals at once - command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_dnascope --step variant_calling --joint_germline --outdir results --sentieon_dnascope_emit_mode gvcf --nucleotides_per_second 100 + command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_dnascope --step variant_calling --joint_germline --outdir results --sentieon_dnascope_emit_mode gvcf --nucleotides_per_second 100 tags: - germline - sentieon/dnascope_joint_germline diff --git a/tests/test_sentieon_dnascope_skip_filter.yml b/tests/test_sentieon_dnascope_skip_filter.yml index 3950f7a438..7c37449a26 100644 --- a/tests/test_sentieon_dnascope_skip_filter.yml +++ b/tests/test_sentieon_dnascope_skip_filter.yml @@ -1,5 +1,5 @@ - name: Run variant calling on germline sample with sentieon dnascope and skip filter - command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --outdir results + command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --outdir results tags: - germline - sentieon/dnascope_skip_filter @@ -43,7 +43,7 @@ md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieon dnascope without intervals and skip filter - command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --no_intervals --outdir results + command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --no_intervals --outdir results tags: - germline - sentieon/dnascope_skip_filter diff --git a/tests/test_sentieon_haplotyper.yml b/tests/test_sentieon_haplotyper.yml index b5f403710b..948e7a37bd 100644 --- a/tests/test_sentieon_haplotyper.yml +++ b/tests/test_sentieon_haplotyper.yml @@ -1,5 +1,5 @@ - name: Run variant calling on germline sample with sentieons haplotyper - command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results + command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results tags: - germline - sentieon/haplotyper @@ -44,7 +44,7 @@ md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons haplotyper without intervals - command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --no_intervals --outdir results + command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --no_intervals --outdir results tags: - germline - sentieon/haplotyper @@ -94,7 +94,7 @@ md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons haplotyper output gvcf - command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode gvcf + command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode gvcf tags: - germline - sentieon/haplotyper @@ -142,7 +142,7 @@ md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons haplotyper output both gvcf and vcf - command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode variant,gvcf + command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode variant,gvcf tags: - germline - sentieon/haplotyper @@ -182,7 +182,7 @@ md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons haplotyper and gatk haplotypecaller - command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller,sentieon_haplotyper --step variant_calling --outdir results + command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller,sentieon_haplotyper --step variant_calling --outdir results tags: - germline - sentieon/haplotyper diff --git a/tests/test_sentieon_haplotyper_joint_germline.yml b/tests/test_sentieon_haplotyper_joint_germline.yml index 9469559f88..1e4d5d82db 100644 --- a/tests/test_sentieon_haplotyper_joint_germline.yml +++ b/tests/test_sentieon_haplotyper_joint_germline.yml @@ -1,5 +1,5 @@ - name: Run joint germline variant calling with sentieon haplotyper - command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf + command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf tags: - germline - sentieon/haplotyper_joint_germline @@ -49,7 +49,7 @@ md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with sentieon haplotyper all intervals at once - command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf --nucleotides_per_second 100 + command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf --nucleotides_per_second 100 tags: - germline - sentieon/haplotyper_joint_germline @@ -97,7 +97,7 @@ md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with sentieon haplotyper with stub for VQSR - command: nextflow run main.nf -profile test_cache,software_license,tools_germline --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf -stub-run + command: nextflow run main.nf -profile test,software_license,tools_germline --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf -stub-run tags: - germline - sentieon/haplotyper_joint_germline diff --git a/tests/test_sentieon_haplotyper_skip_filter.yml b/tests/test_sentieon_haplotyper_skip_filter.yml index f599260b5f..2f8beaba75 100644 --- a/tests/test_sentieon_haplotyper_skip_filter.yml +++ b/tests/test_sentieon_haplotyper_skip_filter.yml @@ -1,5 +1,5 @@ - name: Run variant calling on germline sample with sentieon haplotyper and skip filter - command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --outdir results + command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --outdir results tags: - germline - sentieon/haplotyper_skip_filter @@ -42,7 +42,7 @@ md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieon haplotyper without intervals and skip filter - command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --no_intervals --outdir results + command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --no_intervals --outdir results tags: - germline - sentieon/haplotyper_skip_filter diff --git a/tests/test_skip_all_qc.yml b/tests/test_skip_all_qc.yml index 9e2ef2ceb1..24938562c2 100644 --- a/tests/test_skip_all_qc.yml +++ b/tests/test_skip_all_qc.yml @@ -1,5 +1,5 @@ - name: Run default pipeline with skipping all QC steps - command: nextflow run main.nf -profile test_cache --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results + command: nextflow run main.nf -profile test --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results tags: - default_extended - preprocessing diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml index d683b6952d..23625f5eb9 100644 --- a/tests/test_skip_markduplicates.yml +++ b/tests/test_skip_markduplicates.yml @@ -1,5 +1,5 @@ - name: Run default pipeline with skipping Markduplicates - command: nextflow run main.nf -profile test_cache,skip_markduplicates --outdir results + command: nextflow run main.nf -profile test,skip_markduplicates --outdir results tags: - default_extended - preprocessing @@ -54,7 +54,7 @@ - path: results/preprocessing/mapped/test/test.sorted.bam should_exist: false - name: Run default pipeline with skipping Markduplicates with save_mapped - command: nextflow run main.nf -profile test_cache,skip_markduplicates --save_mapped --outdir results + command: nextflow run main.nf -profile test,skip_markduplicates --save_mapped --outdir results tags: - default_extended - preprocessing @@ -108,7 +108,7 @@ - path: results/preprocessing/mapped/test/test.bam should_exist: false - name: Run default pipeline with skipping Markduplicates with save_mapped & save_output_as_bam - command: nextflow run main.nf -profile test_cache,skip_markduplicates --save_mapped --save_output_as_bam --outdir results + command: nextflow run main.nf -profile test,skip_markduplicates --save_mapped --save_output_as_bam --outdir results tags: - default_extended - preprocessing diff --git a/tests/test_strelka.yml b/tests/test_strelka.yml index 766d9e18c7..e222a00fa5 100644 --- a/tests/test_strelka.yml +++ b/tests/test_strelka.yml @@ -1,5 +1,5 @@ - name: Skip variant calling on matched normal - command: nextflow run main.nf -profile test_cache,variantcalling_channels --tools strelka --only_paired_variant_calling --outdir results + command: nextflow run main.nf -profile test,variantcalling_channels --tools strelka --only_paired_variant_calling --outdir results tags: - somatic - strelka @@ -123,7 +123,7 @@ - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on germline sample with strelka - command: nextflow run main.nf -profile test_cache,tools_germline --tools strelka --outdir results + command: nextflow run main.nf -profile test,tools_germline --tools strelka --outdir results tags: - germline - strelka @@ -162,7 +162,7 @@ md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on germline sample with strelka without intervals - command: nextflow run main.nf -profile test_cache,tools_germline --tools strelka --no_intervals --outdir results + command: nextflow run main.nf -profile test,tools_germline --tools strelka --no_intervals --outdir results tags: - germline - strelka @@ -206,7 +206,7 @@ md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on tumor only sample with strelka - command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools strelka --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka --outdir results tags: - strelka - tumor_only @@ -245,7 +245,7 @@ md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on tumor only sample with strelka without intervals - command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools strelka --no_intervals --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka --no_intervals --outdir results tags: - no_intervals - strelka @@ -289,7 +289,7 @@ md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on somatic sample with strelka - command: nextflow run main.nf -profile test_cache,tools_somatic --tools strelka --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools strelka --outdir results tags: - somatic - strelka @@ -365,7 +365,7 @@ - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with strelka without intervals - command: nextflow run main.nf -profile test_cache,tools_somatic --tools strelka --no_intervals --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools strelka --no_intervals --outdir results tags: - no_intervals - somatic diff --git a/tests/test_strelka_bp.yml b/tests/test_strelka_bp.yml index b813f648d8..d2ec3549e3 100644 --- a/tests/test_strelka_bp.yml +++ b/tests/test_strelka_bp.yml @@ -1,5 +1,5 @@ - name: Run variant calling on somatic sample with Strelka BP - command: nextflow run main.nf -profile test_cache,tools_somatic --tools strelka,manta --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools strelka,manta --outdir results tags: - somatic - strelka_bp @@ -113,7 +113,7 @@ - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with Strelka BP without intervals - command: nextflow run main.nf -profile test_cache,tools_somatic --tools strelka,manta --no_intervals --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools strelka,manta --no_intervals --outdir results tags: - no_intervals - somatic diff --git a/tests/test_tiddit.yml b/tests/test_tiddit.yml index abac99f94b..8d0c5b718c 100644 --- a/tests/test_tiddit.yml +++ b/tests/test_tiddit.yml @@ -1,5 +1,5 @@ - name: Run variant calling on somatic sample with tiddit - command: nextflow run main.nf -profile test_cache,tools_somatic --tools tiddit --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools tiddit --outdir results tags: - tiddit - somatic @@ -69,7 +69,7 @@ - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on germline sample with tiddit - command: nextflow run main.nf -profile test_cache,tools_germline --tools tiddit --outdir results + command: nextflow run main.nf -profile test,tools_germline --tools tiddit --outdir results tags: - tiddit - germline @@ -106,7 +106,7 @@ md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on tumor_only sample with tiddit - command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools tiddit --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --tools tiddit --outdir results tags: - tiddit - tumor_only diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml index 8725ec6a64..23b005ac7a 100644 --- a/tests/test_tools_manually.yml +++ b/tests/test_tools_manually.yml @@ -1,5 +1,5 @@ - name: Run variant calling on somatic samples with ascat - command: nextflow run main.nf -profile test_cache,tools_somatic_ascat --outdir results + command: nextflow run main.nf -profile test,tools_somatic_ascat --outdir results tags: - ascat_manual - manual @@ -59,7 +59,7 @@ - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with mutect2 without intervals - command: nextflow run main.nf -profile test_cache,tools_somatic --tools mutect2 --no_intervals --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools mutect2 --no_intervals --outdir results tags: - mutect2_manual - manual @@ -127,7 +127,7 @@ - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with mutect2 - command: nextflow run main.nf -profile test_cache,tools_somatic --tools mutect2 --outdir results + command: nextflow run main.nf -profile test,tools_somatic --tools mutect2 --outdir results tags: - mutect2_manual - manual @@ -192,7 +192,7 @@ - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run joint calling on tumor only samples with mutect2 - command: nextflow run main.nf -profile test_cache,tools_tumoronly --input tests/csv/3.0/recalibrated_tumoronly_joint.csv --tools mutect2 --joint_mutect2 --outdir results + command: nextflow run main.nf -profile test,tools_tumoronly --input tests/csv/3.0/recalibrated_tumoronly_joint.csv --tools mutect2 --joint_mutect2 --outdir results tags: - mutect2_manual - manual @@ -251,7 +251,7 @@ - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - name: Run joint calling on somatic samples with mutect2 - command: nextflow run main.nf -profile test_cache,tools_somatic --input tests/csv/3.0/recalibrated_somatic_joint.csv --tools mutect2 --joint_mutect2 --outdir results + command: nextflow run main.nf -profile test,tools_somatic --input tests/csv/3.0/recalibrated_somatic_joint.csv --tools mutect2 --joint_mutect2 --outdir results tags: - mutect2_manual - somatic diff --git a/tests/test_tumor_normal_pair.yml b/tests/test_tumor_normal_pair.yml index b616fc2b83..fe1fd5de21 100644 --- a/tests/test_tumor_normal_pair.yml +++ b/tests/test_tumor_normal_pair.yml @@ -1,5 +1,5 @@ - name: Run default pipeline for tumor normal pair - command: nextflow run main.nf -profile test_cache,pair --outdir results + command: nextflow run main.nf -profile test,pair --outdir results tags: - default_extended - preprocessing diff --git a/tests/test_umi.yml b/tests/test_umi.yml index 0034d131d9..69d8cf2433 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -1,5 +1,5 @@ - name: Run UMI test - command: nextflow run main.nf -profile test_cache,umi --outdir results + command: nextflow run main.nf -profile test,umi --outdir results tags: - preprocessing - umi @@ -52,7 +52,7 @@ # text-based file changes md5sums on reruns - name: Run Sentieon-FGBio UMI combination test - command: nextflow run main.nf -profile test_cache,software_license,umi --sentieon_extension --outdir results --aligner "sentieon-bwamem" + command: nextflow run main.nf -profile test,software_license,umi --sentieon_extension --outdir results --aligner "sentieon-bwamem" tags: - preprocessing - umi @@ -61,7 +61,7 @@ contains: - "Sentieon BWA is currently not compatible with FGBio UMI handeling. Please choose a different aligner." # - name: Run UMI TSO test -# command: nextflow run main.nf -profile test_cache,umi_tso --outdir results +# command: nextflow run main.nf -profile test,umi_tso --outdir results # tags: # - umi_tso # - umi From a23a013dcc2a5d6e66eb8ab403bf1928887a2adb Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 29 Apr 2024 14:34:32 +0000 Subject: [PATCH 25/72] Update mosdepth --- modules.json | 2 +- modules/nf-core/mosdepth/environment.yml | 2 +- modules/nf-core/mosdepth/main.nf | 4 +- .../nf-core/mosdepth/tests/main.nf.test.snap | 120 +++++++++--------- 4 files changed, 64 insertions(+), 64 deletions(-) diff --git a/modules.json b/modules.json index 747c53a5f5..dda7cb585b 100644 --- a/modules.json +++ b/modules.json @@ -316,7 +316,7 @@ }, "mosdepth": { "branch": "master", - "git_sha": "30d3ca4346ae38f0de821c57a9c517b8b0b135d6", + "git_sha": "e0616fba0919adb190bfe070d17fb12d76ba3a26", "installed_by": ["modules"] }, "msisensorpro/msisomatic": { diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index 88c7126c05..bcb9d64a7a 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -5,4 +5,4 @@ channels: - defaults dependencies: # renovate: datasource=conda depName=bioconda/mosdepth - - mosdepth=0.3.6 + - mosdepth=0.3.8 diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index 0190a09d80..6f4a838343 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -4,8 +4,8 @@ process MOSDEPTH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.6--hd299d5a_0' : - 'biocontainers/mosdepth:0.3.6--hd299d5a_0'}" + 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.8--hd299d5a_0' : + 'biocontainers/mosdepth:0.3.8--hd299d5a_0'}" input: tuple val(meta), path(bam), path(bai), path(bed) diff --git a/modules/nf-core/mosdepth/tests/main.nf.test.snap b/modules/nf-core/mosdepth/tests/main.nf.test.snap index 00f4cd974b..c604540b03 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test.snap +++ b/modules/nf-core/mosdepth/tests/main.nf.test.snap @@ -39,7 +39,7 @@ ] ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -222,15 +222,15 @@ ] ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:29:04.084192" + "timestamp": "2024-04-29T13:33:16.953408231" }, "homo_sapiens - cram, crai, bed": { "content": [ @@ -260,7 +260,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -289,7 +289,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -307,7 +307,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -340,7 +340,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -367,7 +367,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -395,15 +395,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:28:16.664319" + "timestamp": "2024-04-29T13:32:50.160217828" }, "homo_sapiens - bam, bai, [] - quantized": { "content": [ @@ -433,7 +433,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -456,7 +456,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -480,7 +480,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" + "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" ] ], "global_txt": [ @@ -507,7 +507,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -528,7 +528,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" + "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" ] ], "regions_bed": [ @@ -556,15 +556,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:28:35.978752" + "timestamp": "2024-04-29T13:33:01.164885111" }, "homo_sapiens - bam, bai, bed": { "content": [ @@ -594,7 +594,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -623,7 +623,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -641,7 +641,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -674,7 +674,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -701,7 +701,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -729,15 +729,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:27:55.598384" + "timestamp": "2024-04-29T13:32:39.071657456" }, "homo_sapiens - bam, bai, [] - window": { "content": [ @@ -767,7 +767,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -775,7 +775,7 @@ "id": "test", "single_end": true }, - "test.mosdepth.region.dist.txt:md5,39e0e707ec32feb5176fd20a95f1f468" + "test.mosdepth.region.dist.txt:md5,0b6ea9f0da1228252d9aef2d3b6f7f76" ] ], "3": [ @@ -796,7 +796,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -814,7 +814,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" + "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" ] ], "8": [ @@ -847,7 +847,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -874,7 +874,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" + "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" ] ], "regions_txt": [ @@ -883,7 +883,7 @@ "id": "test", "single_end": true }, - "test.mosdepth.region.dist.txt:md5,39e0e707ec32feb5176fd20a95f1f468" + "test.mosdepth.region.dist.txt:md5,0b6ea9f0da1228252d9aef2d3b6f7f76" ] ], "summary_txt": [ @@ -902,15 +902,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:28:26.37386" + "timestamp": "2024-04-29T13:32:55.631776118" }, "homo_sapiens - bam, bai, []": { "content": [ @@ -940,7 +940,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -963,7 +963,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -1002,7 +1002,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -1039,15 +1039,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:27:44.658599" + "timestamp": "2024-04-29T13:32:33.642125299" }, "homo_sapiens - cram, crai, []": { "content": [ @@ -1077,7 +1077,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -1100,7 +1100,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -1139,7 +1139,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -1176,15 +1176,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:28:06.482838" + "timestamp": "2024-04-29T13:32:44.704920941" }, "homo_sapiens - bam, bai, bed - thresholds": { "content": [ @@ -1222,11 +1222,11 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" + "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" ] ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -1255,7 +1255,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -1273,7 +1273,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -1306,7 +1306,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -1333,7 +1333,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -1369,18 +1369,18 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" + "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" ] ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:28:45.918241" + "timestamp": "2024-04-29T13:33:06.737266831" } } \ No newline at end of file From a9706dfc4f5f268e148dcb97e769158d8e4340dc Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 29 Apr 2024 16:38:18 +0200 Subject: [PATCH 26/72] fix order --- conf/test.config | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/conf/test.config b/conf/test.config index 295b379b8e..7bb4be332a 100644 --- a/conf/test.config +++ b/conf/test.config @@ -18,6 +18,9 @@ params { max_memory = '6.5GB' max_time = '8.h' + // Base directory for nf-core/modules test data + modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' + // Input data input = "${projectDir}/tests/csv/3.0/fastq_single.csv" @@ -42,8 +45,6 @@ params { // Ignore params that will throw warning through params validation validationSchemaIgnoreParams = 'genomes' - // Base directory for nf-core/modules test data - modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' } process { From cc6c66da6828a313dce9d0a6a924d581ed9c2075 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 29 Apr 2024 16:40:32 +0200 Subject: [PATCH 27/72] update CHANGELOG --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f4236d42a7..175546d54f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added +- [#1489](https://github.com/nf-core/sarek/pull/1489) - Added a `testdata.nf-core.sarek` key in `conf/igenomes.config` for small reference + ### Changed - [#1477](https://github.com/nf-core/sarek/pull/1477) - Back to dev @@ -23,6 +25,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Removed +- [#1489](https://github.com/nf-core/sarek/pull/1489) - Remove `test_cache` profile + ### Dependencies | Dependency | Old version | New version | From 8b5d74d63ef1c2f000f860fad7bd6c19c5536f10 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 29 Apr 2024 17:13:25 +0200 Subject: [PATCH 28/72] fai -> fasta_fai --- conf/test/tools.config | 2 +- conf/test/tools_germline.config | 2 +- conf/test/tools_somatic.config | 2 +- conf/test/tools_tumoronly.config | 2 +- conf/test/variantcalling_channels.config | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/conf/test/tools.config b/conf/test/tools.config index 22e5c92d59..1dfd59d9a8 100644 --- a/conf/test/tools.config +++ b/conf/test/tools.config @@ -15,7 +15,7 @@ params { igenomes_ignore = true dbsnp = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" dbsnp_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" - fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" + fasta_fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" germline_resource = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" germline_resource_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" diff --git a/conf/test/tools_germline.config b/conf/test/tools_germline.config index 531f5e9b65..8cd0a21990 100644 --- a/conf/test/tools_germline.config +++ b/conf/test/tools_germline.config @@ -15,8 +15,8 @@ params { igenomes_ignore = true dbsnp = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" dbsnp_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" - fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + fasta_fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" known_indels = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" known_indels_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" diff --git a/conf/test/tools_somatic.config b/conf/test/tools_somatic.config index 6e040c81e8..10a56d1f25 100644 --- a/conf/test/tools_somatic.config +++ b/conf/test/tools_somatic.config @@ -16,8 +16,8 @@ params { chr_dir = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz" dbsnp = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" dbsnp_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" - fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + fasta_fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" germline_resource = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" germline_resource_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" diff --git a/conf/test/tools_tumoronly.config b/conf/test/tools_tumoronly.config index 72e87e6065..f90e23ae22 100644 --- a/conf/test/tools_tumoronly.config +++ b/conf/test/tools_tumoronly.config @@ -15,8 +15,8 @@ params { igenomes_ignore = true dbsnp = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" dbsnp_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" - fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + fasta_fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" germline_resource = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" germline_resource_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" diff --git a/conf/test/variantcalling_channels.config b/conf/test/variantcalling_channels.config index a83ce04ec9..3d13cfbcad 100644 --- a/conf/test/variantcalling_channels.config +++ b/conf/test/variantcalling_channels.config @@ -13,8 +13,8 @@ params { input = "${projectDir}/tests/csv/3.0/recalibrated.csv" genome = null igenomes_ignore = true - fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + fasta_fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" nucleotides_per_second = 20 step = 'variant_calling' From 87cd62ca3fdf6dcde11da38e2285c0c9c305abce Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 29 Apr 2024 17:17:14 +0200 Subject: [PATCH 29/72] fix ngscheckmate bed usage --- conf/test.config | 1 - conf/test/tools.config | 1 + conf/test/tools_germline.config | 1 + conf/test/tools_somatic.config | 1 + conf/test/tools_somatic_ascat.config | 6 +++--- conf/test/tools_tumoronly.config | 1 + conf/test/variantcalling_channels.config | 1 + 7 files changed, 8 insertions(+), 4 deletions(-) diff --git a/conf/test.config b/conf/test.config index 7bb4be332a..9937483d77 100644 --- a/conf/test.config +++ b/conf/test.config @@ -44,7 +44,6 @@ params { // Ignore params that will throw warning through params validation validationSchemaIgnoreParams = 'genomes' - } process { diff --git a/conf/test/tools.config b/conf/test/tools.config index 1dfd59d9a8..a749ae5ea7 100644 --- a/conf/test/tools.config +++ b/conf/test/tools.config @@ -22,6 +22,7 @@ params { intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" pon = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" pon_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" + ngscheckmate_bed = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed" nucleotides_per_second = 20 step = 'variant_calling' tools = null diff --git a/conf/test/tools_germline.config b/conf/test/tools_germline.config index 8cd0a21990..5b8baa1996 100644 --- a/conf/test/tools_germline.config +++ b/conf/test/tools_germline.config @@ -24,6 +24,7 @@ params { known_snps = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz" known_snps_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi" known_snps_vqsr = "--resource:hapmap,known=false,training=true,truth=true,prior=10.0 hapmap_3.3.hg38.vcf.gz" + ngscheckmate_bed = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed" nucleotides_per_second = 20 step = 'variant_calling' tools = null diff --git a/conf/test/tools_somatic.config b/conf/test/tools_somatic.config index 10a56d1f25..2fdff58e16 100644 --- a/conf/test/tools_somatic.config +++ b/conf/test/tools_somatic.config @@ -23,6 +23,7 @@ params { intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" pon = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" pon_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" + ngscheckmate_bed = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed" nucleotides_per_second = 20 step = 'variant_calling' tools = null diff --git a/conf/test/tools_somatic_ascat.config b/conf/test/tools_somatic_ascat.config index 001d543726..ec6df8e483 100644 --- a/conf/test/tools_somatic_ascat.config +++ b/conf/test/tools_somatic_ascat.config @@ -18,7 +18,7 @@ params { chr_dir = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz" germline_resource = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" - step = 'variant_calling' - tools = 'ascat' - wes = false + step = 'variant_calling' + tools = 'ascat' + wes = false } diff --git a/conf/test/tools_tumoronly.config b/conf/test/tools_tumoronly.config index f90e23ae22..daf931d964 100644 --- a/conf/test/tools_tumoronly.config +++ b/conf/test/tools_tumoronly.config @@ -22,6 +22,7 @@ params { intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" pon = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" pon_tbi = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" + ngscheckmate_bed = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed" nucleotides_per_second = 20 step = 'variant_calling' tools = null diff --git a/conf/test/variantcalling_channels.config b/conf/test/variantcalling_channels.config index 3d13cfbcad..572a2e18ea 100644 --- a/conf/test/variantcalling_channels.config +++ b/conf/test/variantcalling_channels.config @@ -16,6 +16,7 @@ params { fasta = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" fasta_fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" + ngscheckmate_bed = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed" nucleotides_per_second = 20 step = 'variant_calling' tools = null From 70ef51c90526c0f13d20d034a5419fd98e3fcbac Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 29 Apr 2024 17:30:49 +0200 Subject: [PATCH 30/72] update and fix tests --- .github/workflows/ci.yml | 3 +++ conf/test.config | 4 ++-- tests/main.nf.test | 4 ---- tests/test_aligner_bwamem.yml | 16 ---------------- tests/test_aligner_bwamem2.yml | 16 ---------------- tests/test_aligner_dragmap.yml | 15 --------------- tests/test_msisensorpro.yml | 8 -------- 7 files changed, 5 insertions(+), 61 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 48fbb4b6b1..0e4d3636c3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -256,6 +256,9 @@ jobs: - tags: "tabix/tabix" - tags: "tiddit/sv" - tags: "untar" + - tags: "pipeline_sarek" + include: + - tags: "test,pipeline_sarek" env: NXF_ANSI_LOG: false TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" diff --git a/conf/test.config b/conf/test.config index 9937483d77..9dd0bca957 100644 --- a/conf/test.config +++ b/conf/test.config @@ -19,13 +19,13 @@ params { max_time = '8.h' // Base directory for nf-core/modules test data - modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' + modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules' // Input data input = "${projectDir}/tests/csv/3.0/fastq_single.csv" // small genome on igenomes - igenomes_base = 's3://ngi-igenomes/testdata/nf-core/modules/' + igenomes_base = 's3://ngi-igenomes/testdata/nf-core/modules' genome = 'testdata.nf-core.sarek' // Small reference genome diff --git a/tests/main.nf.test b/tests/main.nf.test index ad9209ab88..88ca0df8ff 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -13,9 +13,6 @@ nextflow_pipeline { max_cpus = 2 max_memory = '6.GB' max_time = '6.h' - input = "$projectDir/tests/csv/3.0/fastq_pair.csv" - validationSchemaIgnoreParams = 'test_data_base,test_data,genomes' - use_gatk_spark = false } } @@ -25,5 +22,4 @@ nextflow_pipeline { ) } } - } diff --git a/tests/test_aligner_bwamem.yml b/tests/test_aligner_bwamem.yml index fddd7d85df..372911cb81 100644 --- a/tests/test_aligner_bwamem.yml +++ b/tests/test_aligner_bwamem.yml @@ -32,20 +32,12 @@ md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070 - path: results/reference/bwa/genome.sa md5sum: e7cff62b919448a3a3d0fe4aaf427594 - - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi - # conda changes md5sums for test - - path: results/reference/dict/genome.dict - md5sum: 2433fe2ba31257337bf4c4bd4cb8da15 - - path: results/reference/fai/genome.fasta.fai - md5sum: 3520cd30e1b100e55f578db9c855f685 - path: results/reference/intervals/chr22_1-40001.bed md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7 - path: results/reference/intervals/chr22_1-40001.bed.gz md5sum: d3341fa28986c40b24fcc10a079dbb80 - path: results/reference/intervals/genome.bed md5sum: a87dc7d20ebca626f65cc16ff6c97a3e - - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi - # conda changes md5sums for test - path: results/reports/fastqc/test-test_L1 - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] @@ -91,17 +83,9 @@ md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070 - path: results/reference/bwa/genome.sa md5sum: e7cff62b919448a3a3d0fe4aaf427594 - - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi - # conda changes md5sums for test - - path: results/reference/dict/genome.dict - md5sum: 2433fe2ba31257337bf4c4bd4cb8da15 - - path: results/reference/fai/genome.fasta.fai - md5sum: 3520cd30e1b100e55f578db9c855f685 - path: results/reference/intervals/chr22_1-40001.bed md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7 - path: results/reference/intervals/chr22_1-40001.bed.gz md5sum: d3341fa28986c40b24fcc10a079dbb80 - path: results/reference/intervals/genome.bed md5sum: a87dc7d20ebca626f65cc16ff6c97a3e - - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi - # conda changes md5sums for test diff --git a/tests/test_aligner_bwamem2.yml b/tests/test_aligner_bwamem2.yml index 7c70129f35..7b870a7d99 100644 --- a/tests/test_aligner_bwamem2.yml +++ b/tests/test_aligner_bwamem2.yml @@ -32,20 +32,12 @@ md5sum: cd4bdf496eab05228a50c45ee43c1ed0 - path: results/reference/bwamem2/genome.fasta.pac md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070 - - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi - # conda changes md5sums for test - - path: results/reference/dict/genome.dict - md5sum: 2433fe2ba31257337bf4c4bd4cb8da15 - - path: results/reference/fai/genome.fasta.fai - md5sum: 3520cd30e1b100e55f578db9c855f685 - path: results/reference/intervals/chr22_1-40001.bed md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7 - path: results/reference/intervals/chr22_1-40001.bed.gz md5sum: d3341fa28986c40b24fcc10a079dbb80 - path: results/reference/intervals/genome.bed md5sum: a87dc7d20ebca626f65cc16ff6c97a3e - - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi - # conda changes md5sums for test - path: results/reports/fastqc/test-test_L1 - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] @@ -91,17 +83,9 @@ md5sum: cd4bdf496eab05228a50c45ee43c1ed0 - path: results/reference/bwamem2/genome.fasta.pac md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070 - - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi - # conda changes md5sums for test - - path: results/reference/dict/genome.dict - md5sum: 2433fe2ba31257337bf4c4bd4cb8da15 - - path: results/reference/fai/genome.fasta.fai - md5sum: 3520cd30e1b100e55f578db9c855f685 - path: results/reference/intervals/chr22_1-40001.bed md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7 - path: results/reference/intervals/chr22_1-40001.bed.gz md5sum: d3341fa28986c40b24fcc10a079dbb80 - path: results/reference/intervals/genome.bed md5sum: a87dc7d20ebca626f65cc16ff6c97a3e - - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi - # conda changes md5sums for test diff --git a/tests/test_aligner_dragmap.yml b/tests/test_aligner_dragmap.yml index 1b4349b80d..98085b25d0 100644 --- a/tests/test_aligner_dragmap.yml +++ b/tests/test_aligner_dragmap.yml @@ -22,9 +22,6 @@ # binary changes md5sums on reruns - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi - # conda changes md5sums for test - - path: results/reference/dict/genome.dict md5sum: 2433fe2ba31257337bf4c4bd4cb8da15 - path: results/reference/dragmap/hash_table.cfg contains: @@ -49,16 +46,12 @@ md5sum: 294939f1f80aa7f4a70b9b537e4c0f21 - path: results/reference/dragmap/str_table.bin md5sum: 45f7818c4a10fdeed04db7a34b5f9ff1 - - path: results/reference/fai/genome.fasta.fai - md5sum: 3520cd30e1b100e55f578db9c855f685 - path: results/reference/intervals/chr22_1-40001.bed md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7 - path: results/reference/intervals/chr22_1-40001.bed.gz md5sum: d3341fa28986c40b24fcc10a079dbb80 - path: results/reference/intervals/genome.bed md5sum: a87dc7d20ebca626f65cc16ff6c97a3e - - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi - # conda changes md5sums for test - path: results/reports/fastqc/test-test_L1 - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["LB0 27214 1086 322 1037558 20017 100 0 0.687981"] @@ -117,17 +110,9 @@ md5sum: 294939f1f80aa7f4a70b9b537e4c0f21 - path: results/reference/dragmap/str_table.bin md5sum: 45f7818c4a10fdeed04db7a34b5f9ff1 - - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi - # conda changes md5sums for test - - path: results/reference/dict/genome.dict - md5sum: 2433fe2ba31257337bf4c4bd4cb8da15 - - path: results/reference/fai/genome.fasta.fai - md5sum: 3520cd30e1b100e55f578db9c855f685 - path: results/reference/intervals/chr22_1-40001.bed md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7 - path: results/reference/intervals/chr22_1-40001.bed.gz md5sum: d3341fa28986c40b24fcc10a079dbb80 - path: results/reference/intervals/genome.bed md5sum: a87dc7d20ebca626f65cc16ff6c97a3e - - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi - # conda changes md5sums for test diff --git a/tests/test_msisensorpro.yml b/tests/test_msisensorpro.yml index 47962d5fa0..8a462e305b 100644 --- a/tests/test_msisensorpro.yml +++ b/tests/test_msisensorpro.yml @@ -53,19 +53,11 @@ md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070 - path: results/reference/bwa/genome.sa md5sum: e7cff62b919448a3a3d0fe4aaf427594 - - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi - # conda changes md5sums for test - - path: results/reference/dict/genome.dict - md5sum: 2433fe2ba31257337bf4c4bd4cb8da15 - - path: results/reference/fai/genome.fasta.fai - md5sum: 3520cd30e1b100e55f578db9c855f685 - path: results/reference/intervals/chr22_1-40001.bed md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7 - path: results/reference/intervals/chr22_1-40001.bed.gz md5sum: d3341fa28986c40b24fcc10a079dbb80 - path: results/reference/intervals/genome.bed md5sum: a87dc7d20ebca626f65cc16ff6c97a3e - - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi - # conda changes md5sums for test - path: results/reference/msi/genome.msisensor_scan.list md5sum: a7886e7a56a1d7e3be6b4496753fd743 From 67fb4cdc812647a146a98838d41834a00c58e651 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 29 Apr 2024 17:35:57 +0200 Subject: [PATCH 31/72] typo --- tests/test_aligner_dragmap.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/test_aligner_dragmap.yml b/tests/test_aligner_dragmap.yml index 98085b25d0..4aabdf592a 100644 --- a/tests/test_aligner_dragmap.yml +++ b/tests/test_aligner_dragmap.yml @@ -22,7 +22,6 @@ # binary changes md5sums on reruns - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - md5sum: 2433fe2ba31257337bf4c4bd4cb8da15 - path: results/reference/dragmap/hash_table.cfg contains: [ From 3f5532141f4035f2bb372725f405bf78f0de29bc Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 29 Apr 2024 17:37:03 +0200 Subject: [PATCH 32/72] Apply suggestions from code review --- tests/main.nf.test | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/main.nf.test b/tests/main.nf.test index 88ca0df8ff..53e3dc0ca6 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_pipeline { max_cpus = 2 max_memory = '6.GB' max_time = '6.h' + input = "$projectDir/tests/csv/3.0/fastq_pair.csv" } } From 45f116a379724bd3c34aa254c9b72b86bf82e235 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 29 Apr 2024 17:46:35 +0200 Subject: [PATCH 33/72] fix included task --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0e4d3636c3..87b6a6d960 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -259,6 +259,7 @@ jobs: - tags: "pipeline_sarek" include: - tags: "test,pipeline_sarek" + profile: "docker" env: NXF_ANSI_LOG: false TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" From 936d80f8261d229949d0b3f3a2dbdc5991819ecf Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 29 Apr 2024 17:55:24 +0200 Subject: [PATCH 34/72] fix profile --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 87b6a6d960..bd10494805 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -258,8 +258,8 @@ jobs: - tags: "untar" - tags: "pipeline_sarek" include: - - tags: "test,pipeline_sarek" - profile: "docker" + - tags: "pipeline_sarek" + profile: "test,docker" env: NXF_ANSI_LOG: false TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" From f614fdcf944b3d6a1dc835830c9628afb396a831 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 29 Apr 2024 20:07:48 +0200 Subject: [PATCH 35/72] no dbsnp_vqsr --- tests/test_joint_germline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_joint_germline.yml b/tests/test_joint_germline.yml index 8379820f42..fdf503d322 100644 --- a/tests/test_joint_germline.yml +++ b/tests/test_joint_germline.yml @@ -1,5 +1,5 @@ - name: Run joint germline variant calling with haplotypecaller - command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --known_snps_vqsr false --known_indels_vqsr false + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --dbsnp_vqsr false --known_snps_vqsr false --known_indels_vqsr false tags: - germline - joint_germline From c7b428b2273dcd9b96212b8e37c902d24b24bf4f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 29 Apr 2024 22:08:53 +0200 Subject: [PATCH 36/72] fix ALL tests --- tests/test_joint_germline.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_joint_germline.yml b/tests/test_joint_germline.yml index fdf503d322..28269bcc66 100644 --- a/tests/test_joint_germline.yml +++ b/tests/test_joint_germline.yml @@ -1,5 +1,5 @@ - name: Run joint germline variant calling with haplotypecaller - command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --dbsnp_vqsr false --known_snps_vqsr false --known_indels_vqsr false + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --dbsnp_vqsr false --known_snps_vqsr false --known_indels_vqsr false --outdir results tags: - germline - joint_germline @@ -53,7 +53,7 @@ md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with haplotypecaller all intervals at once - command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --nucleotides_per_second 100 + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --dbsnp_vqsr false --known_snps_vqsr false --known_indels_vqsr false --nucleotides_per_second 100 --outdir results tags: - germline - joint_germline From da76e252ac2469e0f88dd7d36efbeedb45e4caf3 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 30 Apr 2024 06:16:03 +0000 Subject: [PATCH 37/72] Updating md5sums in tests --- tests/test_markduplicates_from_bam.yml | 12 ++++++------ tests/test_markduplicates_from_cram.yml | 12 ++++++------ tests/test_save_mapped.yml | 8 ++++---- tests/test_save_output_as_bam_only.yml | 8 ++++---- tests/test_tumor_normal_pair.yml | 16 ++++++++-------- 5 files changed, 28 insertions(+), 28 deletions(-) diff --git a/tests/test_markduplicates_from_bam.yml b/tests/test_markduplicates_from_bam.yml index d6191216bd..dee1fd68c1 100644 --- a/tests/test_markduplicates_from_bam.yml +++ b/tests/test_markduplicates_from_bam.yml @@ -73,23 +73,23 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 + md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 + md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 + md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 + md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats diff --git a/tests/test_markduplicates_from_cram.yml b/tests/test_markduplicates_from_cram.yml index f36619f719..0123826c68 100644 --- a/tests/test_markduplicates_from_cram.yml +++ b/tests/test_markduplicates_from_cram.yml @@ -70,23 +70,23 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 + md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 + md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 + md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 + md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats diff --git a/tests/test_save_mapped.yml b/tests/test_save_mapped.yml index 7868da9d35..a4b10fead3 100644 --- a/tests/test_save_mapped.yml +++ b/tests/test_save_mapped.yml @@ -40,9 +40,9 @@ - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 + md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 + md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt @@ -50,9 +50,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 + md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 + md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_save_output_as_bam_only.yml b/tests/test_save_output_as_bam_only.yml index bc577c0ae8..bd8b19f803 100644 --- a/tests/test_save_output_as_bam_only.yml +++ b/tests/test_save_output_as_bam_only.yml @@ -34,9 +34,9 @@ - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 + md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 + md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt @@ -44,9 +44,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 + md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 + md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_tumor_normal_pair.yml b/tests/test_tumor_normal_pair.yml index b616fc2b83..0be73ea719 100644 --- a/tests/test_tumor_normal_pair.yml +++ b/tests/test_tumor_normal_pair.yml @@ -45,9 +45,9 @@ - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt md5sum: d536456436eb275159b8c6af83213d80 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 38fe39894abe62e38f8ac214cba64f2b + md5sum: 16cda2fae13c766a7f241600966343f4 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: b1c2a861f64e20a94108a6de3b76c582 + md5sum: 05d571f8d51ca6b1bde804d7a6d999af - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt md5sum: 76fa71922a3f748e507c2364c531dfcb - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt @@ -55,9 +55,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: d536456436eb275159b8c6af83213d80 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 38fe39894abe62e38f8ac214cba64f2b + md5sum: 16cda2fae13c766a7f241600966343f4 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b1c2a861f64e20a94108a6de3b76c582 + md5sum: 05d571f8d51ca6b1bde804d7a6d999af - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt md5sum: 2020cf6dfc7ddca020c921dd9f0549b7 - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt @@ -65,9 +65,9 @@ - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt md5sum: 8b991358768cade225470a07cd34f573 - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz - md5sum: 5d67bc6ea9f077abb4fdac3b087c6387 + md5sum: 880c996fce059c19c4551b11b3c6f58e - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi - md5sum: d5f1c9389ecf52ba839e834780a94549 + md5sum: eba5aca0b8f72759192bbdd29330278e - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt md5sum: 2020cf6dfc7ddca020c921dd9f0549b7 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt @@ -75,9 +75,9 @@ - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt md5sum: 8b991358768cade225470a07cd34f573 - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz - md5sum: 5d67bc6ea9f077abb4fdac3b087c6387 + md5sum: 880c996fce059c19c4551b11b3c6f58e - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi - md5sum: d5f1c9389ecf52ba839e834780a94549 + md5sum: eba5aca0b8f72759192bbdd29330278e - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats From b8ba32efbf43e632065574763d3cfffcf8176689 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 30 Apr 2024 06:32:51 +0000 Subject: [PATCH 38/72] Updating md5sums in tests --- tests/test_default.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/test_default.yml b/tests/test_default.yml index 5368cfd9b0..84f14e05f2 100644 --- a/tests/test_default.yml +++ b/tests/test_default.yml @@ -36,9 +36,9 @@ - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 + md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 + md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt @@ -46,9 +46,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 + md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 + md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats From 3aabdd871946df015f5e1cc3bcc5ff0b211f283c Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 30 Apr 2024 07:32:59 +0000 Subject: [PATCH 39/72] Updating md5sums in tests --- tests/test_skip_markduplicates.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml index d683b6952d..a39adefd96 100644 --- a/tests/test_skip_markduplicates.yml +++ b/tests/test_skip_markduplicates.yml @@ -28,9 +28,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 67ac075b077723fb1cce4b026dcdf0af + md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 3230b6808c22d4907d18910f2dc2daf2 + md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt @@ -38,9 +38,9 @@ - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: 67ac075b077723fb1cce4b026dcdf0af + md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: 3230b6808c22d4907d18910f2dc2daf2 + md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats @@ -84,9 +84,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 67ac075b077723fb1cce4b026dcdf0af + md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 3230b6808c22d4907d18910f2dc2daf2 + md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt @@ -94,9 +94,9 @@ - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: 67ac075b077723fb1cce4b026dcdf0af + md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: 3230b6808c22d4907d18910f2dc2daf2 + md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats @@ -138,9 +138,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 67ac075b077723fb1cce4b026dcdf0af + md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 3230b6808c22d4907d18910f2dc2daf2 + md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt @@ -148,9 +148,9 @@ - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: 67ac075b077723fb1cce4b026dcdf0af + md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: 3230b6808c22d4907d18910f2dc2daf2 + md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats From 68404a8199b07c3bc51710efa0abda4113d632a9 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 30 Apr 2024 07:57:02 +0000 Subject: [PATCH 40/72] Update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f4236d42a7..f0c59ee268 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1482](https://github.com/nf-core/sarek/pull/1482) - Pin `nf-prov` plugin to `1.2.2` - [#1485](https://github.com/nf-core/sarek/pull/1485) - Update citation for publication - [#1487](https://github.com/nf-core/sarek/pull/1487) - Update sentieon-modules to Sentieon `202308.02` +- [#1490](https://github.com/nf-core/sarek/pull/1490) - Update mosdepth to `0.3.8` ### Fixed @@ -27,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Dependency | Old version | New version | | ---------- | ----------- | ----------- | +| `mosdepth` | 0.3.6 | 0.3.8 | | `sentieon` | 202308.01 | 202308.02 | ### Modules / Subworkflows From 9a4615a348e655c6c69932d44f5090df03e93961 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 30 Apr 2024 16:08:48 +0200 Subject: [PATCH 41/72] feat(wave): add wave profile --- nextflow.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/nextflow.config b/nextflow.config index e32da2cb94..0a49ab49c8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -247,6 +247,12 @@ profiles { shifter.enabled = false singularity.enabled = false } + wave { + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' + } gitpod { executor.cpus = 4 executor.memory = 8.GB From 4a6f602eb3df58d37b36d73cb8c3f4107e079480 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 30 Apr 2024 16:11:09 +0200 Subject: [PATCH 42/72] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fe9a52fb8e..4959461be9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added - [#1489](https://github.com/nf-core/sarek/pull/1489) - Added a `testdata.nf-core.sarek` key in `conf/igenomes.config` for small reference +- [#1493](https://github.com/nf-core/sarek/pull/1493) - Added a `wave` profile ### Changed From 8b8be842c5bb61dee16a6970c11cc2c74c340a06 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 30 Apr 2024 17:43:45 +0200 Subject: [PATCH 43/72] Update nextflow.config --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index 0a49ab49c8..dfe46747a6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -248,6 +248,7 @@ profiles { singularity.enabled = false } wave { + apptainer.ociAutoPull = true singularity.ociAutoPull = true wave.enabled = true wave.freeze = true From 021ec5ff2c26accac0a79d7d1824b35360cbae95 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 11:20:12 +0200 Subject: [PATCH 44/72] fix(sort): fix issue with sorting false on gcp --- workflows/sarek/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf index 5062470373..d28aabff4c 100644 --- a/workflows/sarek/main.nf +++ b/workflows/sarek/main.nf @@ -879,7 +879,7 @@ workflow SAREK { ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(version_yaml) ch_multiqc_files = ch_multiqc_files.mix(reports) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true)) MULTIQC ( ch_multiqc_files.collect(), From b7e352332b851b97ff154704e47af02f7f379504 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 11:20:55 +0200 Subject: [PATCH 45/72] fix(doi): fix multiple doi print --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index afd58a8cc2..282ff83651 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -280,7 +280,13 @@ 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})" : "" + if (meta.manifest_map.doi) { + def temp_doi_ref = "" + String[] manifest_doi = meta.manifest_map.doi.split(",") + for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref}), " + meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length()-2) + } + 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 From adb0ecd3f00fbdcb9afd83cf2fabed1e45d1279c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 11:21:24 +0200 Subject: [PATCH 46/72] fix(manifest): fix doi in manifest --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index e32da2cb94..447e219cd9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -391,7 +391,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' version = '3.5.0dev' - doi = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425' + doi = '10.12688/f1000research.16665.2,10.1093/nargab/lqae031,10.5281/zenodo.3476425' } // Load modules.config for DSL2 module specific options From c8817f919faf373adc183f65ac445a9e6b75aadb Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 11:42:56 +0200 Subject: [PATCH 47/72] code polish --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index 282ff83651..21ed197041 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -285,10 +285,10 @@ def methodsDescriptionText(mqc_methods_yaml) { String[] manifest_doi = meta.manifest_map.doi.split(",") for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref}), " meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length()-2) + } else { + meta["nodoi_text"] = "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " } - 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"] = "" meta["tool_bibliography"] = "" From ce2460b5dbc20397e87e1fdc1315566a3318be37 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 11:46:52 +0200 Subject: [PATCH 48/72] update CHANGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fe9a52fb8e..eac887999e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1378](https://github.com/nf-core/sarek/pull/1378) - Improve cloud tests launch workflow to use matrix - [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline` +- [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix Cloud Storage objects are immutable on GCP [#1491](https://github.com/nf-core/sarek/issues/1491) +- [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix multiple DOI handling in manifest ### Removed From 9f6903e484aed63d93c2274eb81a29cb1ec07477 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 2 May 2024 12:03:49 +0200 Subject: [PATCH 49/72] Update subworkflows/local/utils_nfcore_sarek_pipeline/main.nf --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index 21ed197041..a9ae9cbe93 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -285,9 +285,8 @@ def methodsDescriptionText(mqc_methods_yaml) { String[] manifest_doi = meta.manifest_map.doi.split(",") for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref}), " meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length()-2) - } else { - meta["nodoi_text"] = "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " - } + } 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"] = "" From 7a8a860b82306f82b1bf2b224d510a9cb41a1456 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 15:07:02 +0200 Subject: [PATCH 50/72] let's keep the space and just handle them --- nextflow.config | 2 +- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 447e219cd9..e32da2cb94 100644 --- a/nextflow.config +++ b/nextflow.config @@ -391,7 +391,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' version = '3.5.0dev' - doi = '10.12688/f1000research.16665.2,10.1093/nargab/lqae031,10.5281/zenodo.3476425' + doi = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425' } // Load modules.config for DSL2 module specific options diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index a9ae9cbe93..fc81f2f67b 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -283,7 +283,7 @@ def methodsDescriptionText(mqc_methods_yaml) { if (meta.manifest_map.doi) { def temp_doi_ref = "" String[] manifest_doi = meta.manifest_map.doi.split(",") - for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref}), " + for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.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.
    • " From 0f682d5fcff664a6a7c0787ad14f9f8013936efa Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 16:12:26 +0200 Subject: [PATCH 51/72] deal with multiple DOI properly --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 2 +- subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index fc81f2f67b..67d455863c 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -282,7 +282,7 @@ def methodsDescriptionText(mqc_methods_yaml) { // Pipeline DOI if (meta.manifest_map.doi) { def temp_doi_ref = "" - String[] manifest_doi = meta.manifest_map.doi.split(",") + String[] manifest_doi = meta.manifest_map.doi.tokenize(",") for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace(" ", "")}), " meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length()-2) } else meta["doi_text"] = "" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index a8b55d6fe1..f70b89fd29 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -65,9 +65,12 @@ def checkProfileProvided(nextflow_cli_args) { // Citation string for pipeline // def workflowCitation() { + def temp_doi_ref = "" + String[] manifest_doi = workflow.manifest.doi.tokenize(",") + for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.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" + From 3c286ea810a07a6562fe58dd9adb955306afe28c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 16:42:07 +0200 Subject: [PATCH 52/72] handle multiple DOI --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index afd58a8cc2..e02794a030 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -280,8 +280,13 @@ 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) { + 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"] = "" From 2e11e72972fae1b8f10efe2eac3926ba4453a63a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 17:48:55 +0200 Subject: [PATCH 53/72] add comments --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 3 +++ 1 file changed, 3 insertions(+) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index e02794a030..10e544e9b8 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -281,6 +281,9 @@ def methodsDescriptionText(mqc_methods_yaml) { // Pipeline DOI 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(" ", "")}), " From f975f0ba5157353eb52310e3b534a802155c49c6 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 17:49:57 +0200 Subject: [PATCH 54/72] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4959461be9..a6a408e031 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1378](https://github.com/nf-core/sarek/pull/1378) - Improve cloud tests launch workflow to use matrix - [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline` +- [#1496](https://github.com/nf-core/sarek/pull/1496) - Fix multiple DOI handling in manifest ### Removed From ca8a00747b6c9eb363eea964a4bef8aec90ece86 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 18:00:10 +0200 Subject: [PATCH 55/72] update nf-core/utils_nfcore_pipeline subworkflow --- modules.json | 2 +- subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 8 +++++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/modules.json b/modules.json index dda7cb585b..a64bdb2c7d 100644 --- a/modules.json +++ b/modules.json @@ -500,7 +500,7 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index a8b55d6fe1..14558c3927 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" + From 6a4a1891f962c5b4c7fdad41b3e542f807c12d64 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 18:26:01 +0200 Subject: [PATCH 56/72] update CHANGELOG --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index eac887999e..5ea71806d7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,7 +24,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1378](https://github.com/nf-core/sarek/pull/1378) - Improve cloud tests launch workflow to use matrix - [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline` - [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix Cloud Storage objects are immutable on GCP [#1491](https://github.com/nf-core/sarek/issues/1491) -- [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix multiple DOI handling in manifest ### Removed From c7138909c308b5ebbc1e62decf1ee817801d413a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 18:27:55 +0200 Subject: [PATCH 57/72] revert changes --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 9 ++------- subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 5 +---- 2 files changed, 3 insertions(+), 11 deletions(-) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index 67d455863c..afd58a8cc2 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -280,13 +280,8 @@ def methodsDescriptionText(mqc_methods_yaml) { meta["manifest_map"] = workflow.manifest.toMap() // Pipeline DOI - if (meta.manifest_map.doi) { - 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(" ", "")}), " - 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.
    • " + meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " // Tool references meta["tool_citations"] = "" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index f70b89fd29..a8b55d6fe1 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -65,12 +65,9 @@ def checkProfileProvided(nextflow_cli_args) { // Citation string for pipeline // def workflowCitation() { - def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace(" ", "")}\n" return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + - temp_doi_ref + "\n" + + " ${workflow.manifest.doi}\n\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + From 28e6b22fac9d45fdccb70e3d7627ee2f88e1b07f Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 3 May 2024 13:11:34 +0200 Subject: [PATCH 58/72] Update subworkflows/local/utils_nfcore_sarek_pipeline/main.nf Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index 10e544e9b8..0bd3c1364d 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -289,7 +289,7 @@ def methodsDescriptionText(mqc_methods_yaml) { 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.
    • " + meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of the pipeline version used.
    • " // Tool references meta["tool_citations"] = "" From b0a8ea59926ef29ca03f6404b55af4d34e11c638 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 3 May 2024 17:07:03 +0200 Subject: [PATCH 59/72] feat(release): prepare release 3.4.2 --- CHANGELOG.md | 5 ++++- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index da6cf18dbb..471bb74630 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,12 +5,15 @@ All notable changes to this project will be documented in this file. 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). -## [dev](https://github.com/nf-core/sarek/tree/dev) - Unreleased +## [3.4.2](https://github.com/nf-core/sarek/releases/tag/3.4.2) - Sájtáristjåhkkå + +Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is one of the few peak in Sweden that cannot be climbed without proper climbing equipments. ### Added - [#1489](https://github.com/nf-core/sarek/pull/1489) - Added a `testdata.nf-core.sarek` key in `conf/igenomes.config` for small reference - [#1493](https://github.com/nf-core/sarek/pull/1493) - Added a `wave` profile +- [#1498](https://github.com/nf-core/sarek/pull/1498) - Prepare release `3.4.2` ### Changed diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index ce1a6e388e..206bd82386 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/sarek/ custom_logo_title: "nf-core/sarek" report_comment: > - This report has been generated by the nf-core/sarek + This report has been generated by the nf-core/sarek analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-sarek-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index dfe46747a6..0cd71cd319 100644 --- a/nextflow.config +++ b/nextflow.config @@ -397,7 +397,7 @@ manifest { description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.5.0dev' + version = '3.4.2' doi = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425' } From e7ae4f8447158990e09c0971d068f46fb88ffd58 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 3 May 2024 18:29:25 +0200 Subject: [PATCH 60/72] fix(tests): remove md5sum for all mosdepth tests + update dependency for these tests --- CHANGELOG.md | 2 + tests/config/pytesttags.yml | 23 +++++++ tests/test_aligner_bwamem.yml | 10 --- tests/test_aligner_bwamem2.yml | 10 --- tests/test_aligner_dragmap.yml | 10 --- tests/test_alignment_to_fastq.yml | 10 --- tests/test_cnvkit.yml | 30 -------- tests/test_controlfreec.yml | 23 ------- tests/test_deepvariant.yml | 9 --- tests/test_default.yml | 10 --- tests/test_fastp.yml | 20 ------ tests/test_freebayes.yml | 68 ------------------- tests/test_gatk4spark.yml | 20 ------ tests/test_haplotypecaller.yml | 9 --- tests/test_haplotypecaller_skip_filter.yml | 9 --- tests/test_intervals.yml | 32 --------- tests/test_joint_germline.yml | 30 -------- tests/test_manta.yml | 36 ---------- tests/test_markduplicates_from_bam.yml | 20 ------ tests/test_markduplicates_from_cram.yml | 20 ------ tests/test_mpileup.yml | 18 ----- tests/test_msisensorpro.yml | 10 --- tests/test_mutect2.yml | 9 --- tests/test_prepare_recalibration_from_bam.yml | 6 -- .../test_prepare_recalibration_from_cram.yml | 9 --- tests/test_recalibrate_from_bam.yml | 9 --- tests/test_recalibrate_from_cram.yml | 9 --- tests/test_save_mapped.yml | 10 --- tests/test_save_output_as_bam_only.yml | 10 --- tests/test_sentieon_aligner_bwamem.yml | 30 -------- tests/test_sentieon_dedup_from_bam.yml | 10 --- tests/test_sentieon_dedup_from_cram.yml | 10 --- tests/test_sentieon_dnascope.yml | 19 ------ tests/test_sentieon_dnascope_skip_filter.yml | 9 --- tests/test_sentieon_haplotyper.yml | 19 ------ ...est_sentieon_haplotyper_joint_germline.yml | 30 -------- .../test_sentieon_haplotyper_skip_filter.yml | 6 -- tests/test_skip_markduplicates.yml | 30 -------- tests/test_strelka.yml | 56 --------------- tests/test_strelka_bp.yml | 18 ----- tests/test_tiddit.yml | 20 ------ tests/test_tools_manually.yml | 48 ------------- tests/test_tumor_normal_pair.yml | 20 ------ tests/test_umi.yml | 10 --- 44 files changed, 25 insertions(+), 801 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index da6cf18dbb..ee79107fe7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,6 +26,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline` - [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix Cloud Storage objects are immutable on GCP [#1491](https://github.com/nf-core/sarek/issues/1491) - [#1496](https://github.com/nf-core/sarek/pull/1496) - Fix multiple DOI handling in manifest +- [#1499](https://github.com/nf-core/sarek/pull/1499) - Remove all md5sum for mosdepth tests +- [#1499](https://github.com/nf-core/sarek/pull/1499) - Add mosdepth dependency to all tests runnning it ### Removed diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml index 0c3c05c554..ac74cb8931 100644 --- a/tests/config/pytesttags.yml +++ b/tests/config/pytesttags.yml @@ -76,6 +76,7 @@ validation_checks: alignment_to_fastq: - conf/modules/alignment_to_fastq.config - modules/nf-core/cat/fastq/** + - modules/nf-core/mosdepth/** - modules/nf-core/samtools/collatefastq/** - modules/nf-core/samtools/merge/** - modules/nf-core/samtools/view/** @@ -92,6 +93,7 @@ umi: - modules/nf-core/fgbio/callmolecularconsensusreads/** - modules/nf-core/fgbio/fastqtobam/** - modules/nf-core/fgbio/groupreadsbyumi/** + - modules/nf-core/mosdepth/** - modules/nf-core/samblaster/** - modules/nf-core/samtools/bam2fq/** - subworkflows/local/fastq_align_bwamem_mem2_dragmap/** @@ -103,6 +105,7 @@ umi: fastp: - conf/modules/trimming.config - modules/nf-core/fastp/** + - modules/nf-core/mosdepth/** - tests/csv/3.0/fastq_single.csv - tests/test_fastp.yml @@ -112,6 +115,7 @@ fastp: bwamem: - conf/modules/aligner.config - modules/nf-core/bwa/mem/** + - modules/nf-core/mosdepth/** - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/** - tests/csv/3.0/fastq_single.csv - tests/test_aligner_bwamem.yml @@ -120,6 +124,7 @@ bwamem: bwamem2: - conf/modules/aligner.config - modules/nf-core/bwamem2/mem/** + - modules/nf-core/mosdepth/** - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/** - tests/csv/3.0/fastq_single.csv - tests/test_aligner_bwamem2.yml @@ -128,6 +133,7 @@ bwamem2: dragmap: - conf/modules/aligner.config - modules/nf-core/dragmap/align/** + - modules/nf-core/mosdepth/** - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/** - tests/csv/3.0/fastq_single.csv - tests/test_aligner_dragmap.yml @@ -174,6 +180,7 @@ prepare_recalibration: - conf/modules/prepare_recalibration.config - modules/nf-core/gatk4/baserecalibrator/** - modules/nf-core/gatk4/gatherbqsrreports/** + - modules/nf-core/mosdepth/** - modules/nf-core/samtools/convert/** - subworkflows/local/bam_baserecalibrator/** - tests/csv/3.0/mapped_single_bam.csv @@ -188,6 +195,7 @@ recalibrate: - modules/nf-core/samtools/convert/** - modules/nf-core/samtools/index/** - modules/nf-core/samtools/merge/** + - modules/nf-core/mosdepth/** - subworkflows/local/bam_applybqsr/** - subworkflows/local/cram_merge_index_samtools/** - tests/csv/3.0/prepare_recalibration_single_bam.csv @@ -201,6 +209,7 @@ intervals: - modules/local/build_intervals/** - modules/local/create_intervals_bed/** - modules/nf-core/gatk4/intervallisttobed/** + - modules/nf-core/mosdepth/** - modules/nf-core/tabix/bgziptabix/** - subworkflows/local/prepare_intervals/** - tests/csv/3.0/fastq_single.csv @@ -215,6 +224,7 @@ gatk4spark: - modules/nf-core/gatk4spark/baserecalibrator/** - modules/nf-core/gatk4/estimatelibrarycomplexity/** - modules/nf-core/gatk4spark/markduplicates/** + - modules/nf-core/mosdepth/** - subworkflows/local/bam_applybqsr_spark/** - subworkflows/local/bam_baserecalibrator_spark/** - subworkflows/local/bam_markduplicates_spark/** @@ -229,6 +239,7 @@ cnvkit: - modules/nf-core/cnvkit/antitarget/** - modules/nf-core/cnvkit/batch/** - modules/nf-core/cnvkit/reference/** + - modules/nf-core/mosdepth/** - subworkflows/local/bam_variant_calling_cnvkit/** - subworkflows/local/bam_variant_calling_germline_all/** - subworkflows/local/bam_variant_calling_somatic_all/** @@ -249,6 +260,7 @@ controlfreec: - modules/nf-core/controlfreec/freec2bed/** - modules/nf-core/controlfreec/freec2circos/** - modules/nf-core/controlfreec/makegraph2/** + - modules/nf-core/mosdepth/** - modules/nf-core/samtools/mpileup/** - subworkflows/local/bam_variant_calling_mpileup/** - subworkflows/local/bam_variant_calling_somatic_all/** @@ -264,6 +276,7 @@ deepvariant: - conf/modules/deepvariant.config - modules/nf-core/deepvariant/** - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/mosdepth/** - modules/nf-core/tabix/tabix/** - subworkflows/local/bam_variant_calling_deepvariant/** - subworkflows/local/bam_variant_calling_germline_all/** @@ -276,6 +289,7 @@ freebayes: - modules/nf-core/bcftools/sort/** - modules/nf-core/freebayes/** - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/mosdepth/** - modules/nf-core/tabix/tabix/** - subworkflows/local/bam_variant_calling_freebayes/** - subworkflows/local/bam_variant_calling_germline_all/** @@ -293,6 +307,7 @@ haplotypecaller: - modules/nf-core/gatk4/filtervarianttranches/** - modules/nf-core/gatk4/haplotypecaller/** - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/mosdepth/** - modules/nf-core/samtools/index/** - modules/nf-core/samtools/merge/** - subworkflows/local/bam_merge_index_samtools/** @@ -379,6 +394,7 @@ joint_germline: - modules/nf-core/gatk4/haplotypecaller/** - modules/nf-core/gatk4/mergevcfs/** - modules/nf-core/gatk4/variantrecalibrator/** + - modules/nf-core/mosdepth/** - modules/nf-core/samtools/index/** - modules/nf-core/samtools/merge/** - subworkflows/local/bam_joint_calling_germline_gatk/** @@ -418,6 +434,7 @@ manta: - modules/nf-core/manta/germline/** - modules/nf-core/manta/somatic/** - modules/nf-core/manta/tumoronly/** + - modules/nf-core/mosdepth/** - subworkflows/local/bam_variant_calling_germline_all/** - subworkflows/local/bam_variant_calling_germline_manta/** - subworkflows/local/bam_variant_calling_somatic_all/** @@ -433,6 +450,7 @@ manta: mpileup: - conf/modules/mpileup.config - modules/nf-core/cat/cat/** + - modules/nf-core/mosdepth/** - modules/nf-core/samtools/mpileup/** - subworkflows/local/bam_variant_calling_germline_all/** - subworkflows/local/bam_variant_calling_mpileup/** @@ -447,6 +465,7 @@ msisensorpro: - conf/modules/msisensorpro.config - modules/nf-core/msisensorpro/msi_somatic/** - modules/nf-core/msisensorpro/scan/** + - modules/nf-core/mosdepth/** - subworkflows/local/bam_variant_calling_somatic_all/** - tests/csv/3.0/recalibrated_somatic.csv - tests/test_msisensorpro.yml @@ -462,6 +481,7 @@ mutect2: - modules/nf-core/gatk4/mergemutectstats/** - modules/nf-core/gatk4/mergevcfs/** - modules/nf-core/gatk4/mutect2/** + - modules/nf-core/mosdepth/** - subworkflows/local/bam_variant_calling_somatic_all/** - subworkflows/local/bam_variant_calling_somatic_mutect2/** - subworkflows/local/bam_variant_calling_tumor_only_all/** @@ -473,6 +493,7 @@ mutect2: strelka: - conf/modules/strelka.config - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/mosdepth/** - modules/nf-core/strelka/germline/** - modules/nf-core/strelka/somatic/** - subworkflows/local/bam_variant_calling_germline_all/** @@ -492,6 +513,7 @@ strelka_bp: - conf/modules/strelka.config - modules/nf-core/gatk4/mergevcfs/** - modules/nf-core/manta/somatic/** + - modules/nf-core/mosdepth/** - modules/nf-core/strelka/somatic/** - subworkflows/local/bam_variant_calling_germline_all/** - subworkflows/local/bam_variant_calling_somatic_all/** @@ -505,6 +527,7 @@ strelka_bp: tiddit: - conf/modules/tiddit.config - modules/nf-core/svdb/merge/**.nf + - modules/nf-core/mosdepth/** - modules/nf-core/tabix/bgziptabix/** - modules/nf-core/tiddit/sv/** - subworkflows/local/bam_variant_calling_germline_all/** diff --git a/tests/test_aligner_bwamem.yml b/tests/test_aligner_bwamem.yml index 372911cb81..ccd81021ef 100644 --- a/tests/test_aligner_bwamem.yml +++ b/tests/test_aligner_bwamem.yml @@ -42,25 +42,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_aligner_bwamem2.yml b/tests/test_aligner_bwamem2.yml index 7b870a7d99..be19c08df6 100644 --- a/tests/test_aligner_bwamem2.yml +++ b/tests/test_aligner_bwamem2.yml @@ -42,25 +42,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_aligner_dragmap.yml b/tests/test_aligner_dragmap.yml index 4aabdf592a..6f38538926 100644 --- a/tests/test_aligner_dragmap.yml +++ b/tests/test_aligner_dragmap.yml @@ -55,25 +55,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["LB0 27214 1086 322 1037558 20017 100 0 0.687981"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b0d7d5de1e00132bb5b47e1b3d90d944 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 02b88d7ec0ca8ff23ba688c35939fa05 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 1792d98676f597f755749f4286c5102d - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 590119568d091ce3a88f7fe4f43f24ff - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 2e7fe057ead0622e6a2a6b0ed1832315 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b0d7d5de1e00132bb5b47e1b3d90d944 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 02b88d7ec0ca8ff23ba688c35939fa05 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 1792d98676f597f755749f4286c5102d - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 590119568d091ce3a88f7fe4f43f24ff - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 2e7fe057ead0622e6a2a6b0ed1832315 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_alignment_to_fastq.yml b/tests/test_alignment_to_fastq.yml index 1b64f422e8..bc7a3e5057 100644 --- a/tests/test_alignment_to_fastq.yml +++ b/tests/test_alignment_to_fastq.yml @@ -25,25 +25,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986 1178 1178", "2.0 1.47674 800 800", "100.0 1.911145 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 9cb9b181119256ed17a77dcf44d58285 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: dbe376360e437c89190139ef0ae6769a - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: d9b53915d473710ff0260a0ff694fd32 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: d0713716f63ac573f4a3385733e9a537 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 9cb9b181119256ed17a77dcf44d58285 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: dbe376360e437c89190139ef0ae6769a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d9b53915d473710ff0260a0ff694fd32 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: d0713716f63ac573f4a3385733e9a537 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_cnvkit.yml b/tests/test_cnvkit.yml index 87adbc33c6..43828e540e 100644 --- a/tests/test_cnvkit.yml +++ b/tests/test_cnvkit.yml @@ -58,27 +58,17 @@ - path: results/cnvkit should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on tumor_only sample with cnvkit @@ -113,15 +103,10 @@ - path: results/cnvkit should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on germline sample with cnvkit command: nextflow run main.nf -profile test,tools_germline --tools cnvkit --outdir results @@ -157,15 +142,10 @@ - path: results/cnvkit should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal command: nextflow run main.nf -profile test,tools_somatic --tools cnvkit --only_paired_variant_calling --outdir results @@ -203,26 +183,16 @@ - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn md5sum: b4a49faf170e436ec32dcc21ccc3ce8f - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test diff --git a/tests/test_controlfreec.yml b/tests/test_controlfreec.yml index c3353561a0..d72b67ed27 100644 --- a/tests/test_controlfreec.yml +++ b/tests/test_controlfreec.yml @@ -51,27 +51,17 @@ - path: results/cnvkit should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic samples with controlfreec without intervals @@ -127,23 +117,15 @@ - path: results/mpileup should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample3/sample3.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample4/sample4.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on tumor_only sample with controlfreec @@ -190,13 +172,8 @@ - path: results/mpileup should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample2/sample2.recal.region.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample2/sample2.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/sample2/sample2.recal.cram.stats diff --git a/tests/test_deepvariant.yml b/tests/test_deepvariant.yml index 42660bd78a..d66f2e1aef 100644 --- a/tests/test_deepvariant.yml +++ b/tests/test_deepvariant.yml @@ -25,15 +25,10 @@ - path: results/deepvariant should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on germline sample with deepvariant without intervals command: nextflow run main.nf -profile test,tools_germline --tools deepvariant --no_intervals --outdir results @@ -69,11 +64,7 @@ - path: results/deepvariant should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample1/sample1.recal.cram.stats diff --git a/tests/test_default.yml b/tests/test_default.yml index 84f14e05f2..97ebb3918d 100644 --- a/tests/test_default.yml +++ b/tests/test_default.yml @@ -30,25 +30,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_fastp.yml b/tests/test_fastp.yml index e8fe306468..20eab4065f 100644 --- a/tests/test_fastp.yml +++ b/tests/test_fastp.yml @@ -31,25 +31,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 16608 1860 160 1046616 12117 256 0 0.621261"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 3098d33090a0f90f6fc16d497d2ce644 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 057a02943301a5acec55d19a5a629f11 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: fef22f026f7b4a89ab60c715689c5591 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: cca0f725bea04688b39f2ea8ad2e1605 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: a5ad8f917979f62eacfff1461529dbaa - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 3098d33090a0f90f6fc16d497d2ce644 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 057a02943301a5acec55d19a5a629f11 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: fef22f026f7b4a89ab60c715689c5591 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: cca0f725bea04688b39f2ea8ad2e1605 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: a5ad8f917979f62eacfff1461529dbaa - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -90,25 +80,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17482 890 170 1047682 12552 69 0 0.65881"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 3626e543b91aa564f0056747827366d3 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: e3442f1098899a22748d07ef436925f6 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 2873e7f9c9aede39942731894a6077d1 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 948108074663677f9225fd0574658ca1 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: d5f1c9389ecf52ba839e834780a94549 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 3626e543b91aa564f0056747827366d3 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: e3442f1098899a22748d07ef436925f6 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 2873e7f9c9aede39942731894a6077d1 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 948108074663677f9225fd0574658ca1 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: d5f1c9389ecf52ba839e834780a94549 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_freebayes.yml b/tests/test_freebayes.yml index 6809ac0b4e..d4d85f0a1f 100644 --- a/tests/test_freebayes.yml +++ b/tests/test_freebayes.yml @@ -30,33 +30,19 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: e4ce28ba1c331dc08bc53a0189908f77 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 04d9f20dc5306990eec982a3c5a7d107 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 70b4bbe29bd5e7c4ea39b6caf3316096 - path: results/reports/mosdepth/test/test.md.per-base.bed.gz - md5sum: 2a0c38fb19d6a1f81ca2018e59e7bfcf - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi - md5sum: 0714f8c677277168b9f95d3a43ea5237 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: eb0bc92c253326a109e73af98c9a7d4b - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 9c1d90e0fed14b710098b7724b602aea - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 04d9f20dc5306990eec982a3c5a7d107 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 17dfb78b147488eb8fd450294de4a35e - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: fb6804911f9d437d0251869fe112a528 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 033032cdbb3a2b74dd41dac89628112c - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: eb0bc92c253326a109e73af98c9a7d4b - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -111,25 +97,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -191,61 +167,33 @@ - path: results/reports/markduplicates/test2/test2.md.cram.metrics contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 5a0679057c530e5945c9c5a3a17312dc - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: dcc9ab2bf3248903e02d8da87e678977 - path: results/reports/mosdepth/test/test.md.per-base.bed.gz - md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi - md5sum: b0ab630c3241fbd7581b7a38d944ff8b - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 91e0d531f1bab64711ecefe52bfc8255 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 0b3162def977123809598639f7698121 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: a8455eb2947de529abfa62b303986e0f - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: d9fa560ff78ae106cfee9db2c90801b5 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 4816eeb9af254ca40177b08cf11b98d2 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 91e0d531f1bab64711ecefe52bfc8255 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt - md5sum: f25166c3a0051bb4d8c11a210278de6c - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt - md5sum: 3211135329e4077bd9bf0ba488e14371 - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt - md5sum: ce0eb6d33c6d0dc720fbc6d1811abef8 - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz - md5sum: 55c160e8f3c8c7761524646426611f6b - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz.csi - md5sum: 4205a09ede17cdbdaad45e3553f73105 - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz - md5sum: 1dd426a45f967a9f37dcddcaea29a582 - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt - md5sum: a1ef7e662ce993da4668e804952014ce - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt - md5sum: 3211135329e4077bd9bf0ba488e14371 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt - md5sum: 70ad653c0c98baeeaf5085f1209a7bdb - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz - md5sum: 250a9f15a7d3f102435fa98adccf48a3 - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi - md5sum: 8072f447199c60f24b01eede8b557333 - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz - md5sum: 1dd426a45f967a9f37dcddcaea29a582 - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -328,37 +276,21 @@ - path: results/reports/markduplicates/test2/test2.md.cram.metrics contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 5a0679057c530e5945c9c5a3a17312dc - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 0010c2396a3173c7cf4983abe2eb6a4c - path: results/reports/mosdepth/test/test.md.per-base.bed.gz - md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi - md5sum: b0ab630c3241fbd7581b7a38d944ff8b - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 5a0679057c530e5945c9c5a3a17312dc - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 0010c2396a3173c7cf4983abe2eb6a4c - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: b0ab630c3241fbd7581b7a38d944ff8b - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt - md5sum: f25166c3a0051bb4d8c11a210278de6c - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt - md5sum: d5e4084de2ea2a0a7b60b2d71c804d4b - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz - md5sum: 55c160e8f3c8c7761524646426611f6b - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz.csi - md5sum: 4205a09ede17cdbdaad45e3553f73105 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt - md5sum: f25166c3a0051bb4d8c11a210278de6c - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt - md5sum: d5e4084de2ea2a0a7b60b2d71c804d4b - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz - md5sum: 55c160e8f3c8c7761524646426611f6b - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi - md5sum: 4205a09ede17cdbdaad45e3553f73105 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_gatk4spark.yml b/tests/test_gatk4spark.yml index 270bbdd775..223c5699a4 100644 --- a/tests/test_gatk4spark.yml +++ b/tests/test_gatk4spark.yml @@ -25,23 +25,14 @@ - path: results/reports/markduplicates/test2/test2.md.cram.metrics # text-based file changes md5sums on reruns - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt - md5sum: 85d38a74ce189b9110c57cd94bc26757 - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt - md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81 - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt - md5sum: 04b69ef7f00199dcea7822a79d2c7bd7 - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz - md5sum: 4e6c360aea7f05d801b2ea5685fe154a - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi - md5sum: 5bf5fc178e4faf2462427502c3666004 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt - md5sum: 85d38a74ce189b9110c57cd94bc26757 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt - md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt - md5sum: 04b69ef7f00199dcea7822a79d2c7bd7 - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz - md5sum: 4e6c360aea7f05d801b2ea5685fe154a - path: results/reports/samtools/test2/test2.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test2/test2.recal.cram.stats @@ -78,7 +69,6 @@ - path: results/reports/markduplicates should_exist: false - path: results/reports/mosdepth - should_exist: false - path: results/reports/samtools should_exist: false - name: Run save_output_as_bam with gatk4 spark @@ -109,25 +99,15 @@ - path: results/reports/markduplicates/test2/test2.md.cram.metrics # text-based file changes md5sums on reruns - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt - md5sum: 85d38a74ce189b9110c57cd94bc26757 - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt - md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81 - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt - md5sum: 04b69ef7f00199dcea7822a79d2c7bd7 - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz - md5sum: 4e6c360aea7f05d801b2ea5685fe154a - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi - md5sum: 5bf5fc178e4faf2462427502c3666004 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt - md5sum: 85d38a74ce189b9110c57cd94bc26757 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt - md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt - md5sum: 04b69ef7f00199dcea7822a79d2c7bd7 - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz - md5sum: 4e6c360aea7f05d801b2ea5685fe154a - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi - md5sum: 5bf5fc178e4faf2462427502c3666004 - path: results/reports/samtools/test2/test2.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test2/test2.recal.cram.stats diff --git a/tests/test_haplotypecaller.yml b/tests/test_haplotypecaller.yml index 937198c429..7912e49909 100644 --- a/tests/test_haplotypecaller.yml +++ b/tests/test_haplotypecaller.yml @@ -35,15 +35,10 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with haplotypecaller without intervals @@ -90,11 +85,7 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 4f0d231060cbde4efdd673863bd2fb59 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_haplotypecaller_skip_filter.yml b/tests/test_haplotypecaller_skip_filter.yml index 5741547e4f..b96157f868 100644 --- a/tests/test_haplotypecaller_skip_filter.yml +++ b/tests/test_haplotypecaller_skip_filter.yml @@ -39,15 +39,10 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with haplotypecaller without intervals and skip filter command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --skip_tools haplotypecaller_filter --no_intervals --outdir results @@ -93,11 +88,7 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 4f0d231060cbde4efdd673863bd2fb59 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_intervals.yml b/tests/test_intervals.yml index df0abfdfa0..21326859d3 100644 --- a/tests/test_intervals.yml +++ b/tests/test_intervals.yml @@ -26,33 +26,19 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: e4ce28ba1c331dc08bc53a0189908f77 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 04d9f20dc5306990eec982a3c5a7d107 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 70b4bbe29bd5e7c4ea39b6caf3316096 - path: results/reports/mosdepth/test/test.md.per-base.bed.gz - md5sum: 2a0c38fb19d6a1f81ca2018e59e7bfcf - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi - md5sum: 0714f8c677277168b9f95d3a43ea5237 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: eb0bc92c253326a109e73af98c9a7d4b - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 9c1d90e0fed14b710098b7724b602aea - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 04d9f20dc5306990eec982a3c5a7d107 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 17dfb78b147488eb8fd450294de4a35e - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: fb6804911f9d437d0251869fe112a528 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 033032cdbb3a2b74dd41dac89628112c - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: eb0bc92c253326a109e73af98c9a7d4b - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -89,21 +75,13 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -142,25 +120,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_joint_germline.yml b/tests/test_joint_germline.yml index 28269bcc66..badaf3c807 100644 --- a/tests/test_joint_germline.yml +++ b/tests/test_joint_germline.yml @@ -31,26 +31,16 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testN/testN.recal.cram.stats - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt - md5sum: ba97ed85645f77da6f3adad138b3cdb4 - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt - md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt - md5sum: a937108cbf24c1430b79c861234ce22b - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz - md5sum: d2b579a74bf8d858f82869f073056252 - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with haplotypecaller all intervals at once command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --dbsnp_vqsr false --known_snps_vqsr false --known_indels_vqsr false --nucleotides_per_second 100 --outdir results @@ -85,26 +75,16 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testN/testN.recal.cram.stats - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt - md5sum: ba97ed85645f77da6f3adad138b3cdb4 - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt - md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt - md5sum: a937108cbf24c1430b79c861234ce22b - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz - md5sum: d2b579a74bf8d858f82869f073056252 - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with haplotypecaller with Stub for VQSR command: nextflow run main.nf -profile test,tools_germline --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results -stub-run @@ -144,24 +124,14 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/testN/testN.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testN/testN.recal.region.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testN/testN.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/testN/testN.recal.cram.stats - path: results/reports/mosdepth/testT/testT.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testT/testT.recal.region.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testT/testT.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/testT/testT.recal.cram.stats diff --git a/tests/test_manta.yml b/tests/test_manta.yml index 2d4fefe378..8b9dfbd168 100644 --- a/tests/test_manta.yml +++ b/tests/test_manta.yml @@ -23,15 +23,10 @@ - path: results/manta should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on germline sample with manta without intervals command: nextflow run main.nf -profile test,tools_germline --tools manta --no_intervals --outdir results @@ -65,13 +60,9 @@ - path: results/manta should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on tumor_only sample with manta command: nextflow run main.nf -profile test,tools_tumoronly --tools manta --outdir results @@ -98,15 +89,10 @@ - path: results/manta should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on tumor_only sample with manta without intervals command: nextflow run main.nf -profile test,tools_tumoronly --tools manta --no_intervals --outdir results @@ -140,13 +126,9 @@ - path: results/manta should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on somatic sample with manta command: nextflow run main.nf -profile test,tools_somatic --tools manta --outdir results @@ -197,27 +179,17 @@ - path: results/manta should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with manta without intervals @@ -276,22 +248,14 @@ - path: results/manta should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test diff --git a/tests/test_markduplicates_from_bam.yml b/tests/test_markduplicates_from_bam.yml index 1619bc2545..ab436a7ce2 100644 --- a/tests/test_markduplicates_from_bam.yml +++ b/tests/test_markduplicates_from_bam.yml @@ -25,25 +25,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986 1178 1178", "100.0 1.911145 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -71,25 +61,15 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats diff --git a/tests/test_markduplicates_from_cram.yml b/tests/test_markduplicates_from_cram.yml index e70d9e2325..ff28636112 100644 --- a/tests/test_markduplicates_from_cram.yml +++ b/tests/test_markduplicates_from_cram.yml @@ -25,25 +25,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986 1178 1178", "100.0 1.911145 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -68,25 +58,15 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats diff --git a/tests/test_mpileup.yml b/tests/test_mpileup.yml index 25fefd0eb0..c6603211b3 100644 --- a/tests/test_mpileup.yml +++ b/tests/test_mpileup.yml @@ -14,15 +14,10 @@ - path: results/mpileup should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on tumor_only sample to test mpileup without intervals command: nextflow run main.nf -profile test,tools_tumoronly --tools mpileup --no_intervals --outdir results @@ -47,13 +42,9 @@ - path: results/mpileup should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on germline sample to test mpileup command: nextflow run main.nf -profile test,tools_germline --tools mpileup --outdir results @@ -71,15 +62,10 @@ - path: results/mpileup should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on germline sample to test mpileup without intervals command: nextflow run main.nf -profile test,tools_germline --tools mpileup --no_intervals --outdir results @@ -104,11 +90,7 @@ - path: results/mpileup should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample1/sample1.recal.cram.stats diff --git a/tests/test_msisensorpro.yml b/tests/test_msisensorpro.yml index 8a462e305b..5133de900b 100644 --- a/tests/test_msisensorpro.yml +++ b/tests/test_msisensorpro.yml @@ -13,27 +13,17 @@ - path: results/msisensorpro should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Build only index with msisensorpro diff --git a/tests/test_mutect2.yml b/tests/test_mutect2.yml index 28d9f5f933..c5ea0e8b8d 100644 --- a/tests/test_mutect2.yml +++ b/tests/test_mutect2.yml @@ -39,15 +39,10 @@ - path: results/mutect2 should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on tumor only sample with mutect2 without intervals command: nextflow run main.nf -profile test,tools_tumoronly --tools mutect2 --no_intervals --outdir results @@ -97,11 +92,7 @@ - path: results/mutect2 should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample2/sample2.recal.cram.stats diff --git a/tests/test_prepare_recalibration_from_bam.yml b/tests/test_prepare_recalibration_from_bam.yml index b5ab788e78..7095fe98a0 100644 --- a/tests/test_prepare_recalibration_from_bam.yml +++ b/tests/test_prepare_recalibration_from_bam.yml @@ -21,15 +21,10 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/preprocessing/mapped/ @@ -75,7 +70,6 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth - should_exist: false - path: results/reports/samtools_stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_prepare_recalibration_from_cram.yml b/tests/test_prepare_recalibration_from_cram.yml index d207c6f190..c002b299c3 100644 --- a/tests/test_prepare_recalibration_from_cram.yml +++ b/tests/test_prepare_recalibration_from_cram.yml @@ -15,15 +15,10 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/preprocessing/mapped/ @@ -69,13 +64,9 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - should_exist: false - path: results/reports/samtools/test/test.recal.cram.stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_recalibrate_from_bam.yml b/tests/test_recalibrate_from_bam.yml index 41d0c91e4a..4edc5161dd 100644 --- a/tests/test_recalibrate_from_bam.yml +++ b/tests/test_recalibrate_from_bam.yml @@ -17,15 +17,10 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/preprocessing/mapped/ @@ -72,13 +67,9 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - should_exist: false - path: results/reports/samtools/test/test.recal.cram.stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_recalibrate_from_cram.yml b/tests/test_recalibrate_from_cram.yml index 5f5d0badd3..779fbb148f 100644 --- a/tests/test_recalibrate_from_cram.yml +++ b/tests/test_recalibrate_from_cram.yml @@ -13,15 +13,10 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/preprocessing/mapped/ @@ -68,13 +63,9 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - should_exist: false - path: results/reports/samtools/test/test.recal.cram.stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_save_mapped.yml b/tests/test_save_mapped.yml index f7f7005724..251e7ddacc 100644 --- a/tests/test_save_mapped.yml +++ b/tests/test_save_mapped.yml @@ -34,25 +34,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_save_output_as_bam_only.yml b/tests/test_save_output_as_bam_only.yml index ffcf66e331..6e47260424 100644 --- a/tests/test_save_output_as_bam_only.yml +++ b/tests/test_save_output_as_bam_only.yml @@ -28,25 +28,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_aligner_bwamem.yml b/tests/test_sentieon_aligner_bwamem.yml index 6bf048cecb..36f5e66683 100644 --- a/tests/test_sentieon_aligner_bwamem.yml +++ b/tests/test_sentieon_aligner_bwamem.yml @@ -50,25 +50,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 9afbcd5e44b62b3947e47af850a66188 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 3bd6a6f7127394802d9a7c7d559072ee - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 72ae14370dfdaab906e50d0552c90119 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 9afbcd5e44b62b3947e47af850a66188 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 3bd6a6f7127394802d9a7c7d559072ee - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 72ae14370dfdaab906e50d0552c90119 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -136,25 +126,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 9afbcd5e44b62b3947e47af850a66188 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 3bd6a6f7127394802d9a7c7d559072ee - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 72ae14370dfdaab906e50d0552c90119 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 9afbcd5e44b62b3947e47af850a66188 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 3bd6a6f7127394802d9a7c7d559072ee - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 72ae14370dfdaab906e50d0552c90119 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -190,25 +170,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 9afbcd5e44b62b3947e47af850a66188 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 3bd6a6f7127394802d9a7c7d559072ee - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 72ae14370dfdaab906e50d0552c90119 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 9afbcd5e44b62b3947e47af850a66188 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 3bd6a6f7127394802d9a7c7d559072ee - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 72ae14370dfdaab906e50d0552c90119 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_dedup_from_bam.yml b/tests/test_sentieon_dedup_from_bam.yml index 306ae5634f..48d55177e0 100644 --- a/tests/test_sentieon_dedup_from_bam.yml +++ b/tests/test_sentieon_dedup_from_bam.yml @@ -27,25 +27,15 @@ - path: results/reports/sentieon_dedup/test/test.dedup.cram.metrics contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986", "100.0 1.911145"] - path: results/reports/mosdepth/test/test.dedup.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.dedup.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.dedup.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.dedup.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.dedup.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/samtools/test/test.dedup.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_dedup_from_cram.yml b/tests/test_sentieon_dedup_from_cram.yml index abf6f57da6..9f826c502c 100644 --- a/tests/test_sentieon_dedup_from_cram.yml +++ b/tests/test_sentieon_dedup_from_cram.yml @@ -27,25 +27,15 @@ - path: results/reports/sentieon_dedup/test/test.dedup.cram.metrics contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986", "2.0 1.476740", "3.0 1.704038"] - path: results/reports/mosdepth/test/test.dedup.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.dedup.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.dedup.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.dedup.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.dedup.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/samtools/test/test.dedup.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_dnascope.yml b/tests/test_sentieon_dnascope.yml index 889954b90e..142cd73156 100644 --- a/tests/test_sentieon_dnascope.yml +++ b/tests/test_sentieon_dnascope.yml @@ -34,15 +34,10 @@ - path: results/dnascope should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons dnascope without intervals command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --no_intervals --outdir results @@ -87,13 +82,9 @@ - path: results/sentieon_dnascope should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 4f0d231060cbde4efdd673863bd2fb59 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons dnascope output gvcf @@ -135,15 +126,10 @@ - path: results/dnascope should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons dnascope output both gvcf and vcf command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode variant,gvcf @@ -176,13 +162,8 @@ - path: results/dnascope should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_dnascope_skip_filter.yml b/tests/test_sentieon_dnascope_skip_filter.yml index 7c37449a26..b3740ca749 100644 --- a/tests/test_sentieon_dnascope_skip_filter.yml +++ b/tests/test_sentieon_dnascope_skip_filter.yml @@ -32,15 +32,10 @@ - path: results/sentieon_dnascope should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieon dnascope without intervals and skip filter command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --no_intervals --outdir results @@ -83,11 +78,7 @@ - path: results/sentieon_dnascope should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 4f0d231060cbde4efdd673863bd2fb59 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_haplotyper.yml b/tests/test_sentieon_haplotyper.yml index 948e7a37bd..201d07a5be 100644 --- a/tests/test_sentieon_haplotyper.yml +++ b/tests/test_sentieon_haplotyper.yml @@ -34,14 +34,10 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons haplotyper without intervals command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --no_intervals --outdir results @@ -86,12 +82,9 @@ - path: results/sentieon_haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons haplotyper output gvcf command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode gvcf @@ -132,14 +125,10 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons haplotyper output both gvcf and vcf command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode variant,gvcf @@ -172,14 +161,10 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons haplotyper and gatk haplotypecaller command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller,sentieon_haplotyper --step variant_calling --outdir results @@ -225,12 +210,8 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_haplotyper_joint_germline.yml b/tests/test_sentieon_haplotyper_joint_germline.yml index 1e4d5d82db..7dfa2d5d1d 100644 --- a/tests/test_sentieon_haplotyper_joint_germline.yml +++ b/tests/test_sentieon_haplotyper_joint_germline.yml @@ -27,26 +27,16 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testN/testN.recal.cram.stats - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt - md5sum: ba97ed85645f77da6f3adad138b3cdb4 - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt - md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt - md5sum: a937108cbf24c1430b79c861234ce22b - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz - md5sum: d2b579a74bf8d858f82869f073056252 - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with sentieon haplotyper all intervals at once command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf --nucleotides_per_second 100 @@ -75,26 +65,16 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testN/testN.recal.cram.stats - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt - md5sum: ba97ed85645f77da6f3adad138b3cdb4 - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt - md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt - md5sum: a937108cbf24c1430b79c861234ce22b - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz - md5sum: d2b579a74bf8d858f82869f073056252 - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with sentieon haplotyper with stub for VQSR command: nextflow run main.nf -profile test,software_license,tools_germline --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf -stub-run @@ -123,24 +103,14 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/testN/testN.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testN/testN.recal.region.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testN/testN.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/testN/testN.recal.cram.stats - path: results/reports/mosdepth/testT/testT.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testT/testT.recal.region.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testT/testT.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/testT/testT.recal.cram.stats diff --git a/tests/test_sentieon_haplotyper_skip_filter.yml b/tests/test_sentieon_haplotyper_skip_filter.yml index 2f8beaba75..7328e9a4ec 100644 --- a/tests/test_sentieon_haplotyper_skip_filter.yml +++ b/tests/test_sentieon_haplotyper_skip_filter.yml @@ -34,12 +34,9 @@ - path: results/sentieon_haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieon haplotyper without intervals and skip filter command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --no_intervals --outdir results @@ -84,10 +81,7 @@ - path: results/sentieon_haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml index cde62c04d2..93718954c8 100644 --- a/tests/test_skip_markduplicates.yml +++ b/tests/test_skip_markduplicates.yml @@ -22,25 +22,15 @@ # binary changes md5sums on reruns - path: results/reports/fastqc/test-test_L1 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1653d9aa161a78d8574269083f7d92f1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 1653d9aa161a78d8574269083f7d92f1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats @@ -78,25 +68,15 @@ # binary changes md5sums on reruns - path: results/reports/fastqc/test-test_L1 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1653d9aa161a78d8574269083f7d92f1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 1653d9aa161a78d8574269083f7d92f1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats @@ -132,25 +112,15 @@ # binary changes md5sums on reruns - path: results/reports/fastqc/test-test_L1 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1653d9aa161a78d8574269083f7d92f1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 1653d9aa161a78d8574269083f7d92f1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats diff --git a/tests/test_strelka.yml b/tests/test_strelka.yml index e222a00fa5..b2b25672a2 100644 --- a/tests/test_strelka.yml +++ b/tests/test_strelka.yml @@ -77,49 +77,29 @@ - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on germline sample with strelka @@ -151,15 +131,10 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on germline sample with strelka without intervals command: nextflow run main.nf -profile test,tools_germline --tools strelka --no_intervals --outdir results @@ -197,13 +172,9 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on tumor only sample with strelka command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka --outdir results @@ -234,15 +205,10 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on tumor only sample with strelka without intervals command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka --no_intervals --outdir results @@ -280,13 +246,9 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on somatic sample with strelka command: nextflow run main.nf -profile test,tools_somatic --tools strelka --outdir results @@ -341,27 +303,17 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with strelka without intervals @@ -424,22 +376,14 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test diff --git a/tests/test_strelka_bp.yml b/tests/test_strelka_bp.yml index d2ec3549e3..f5954de37c 100644 --- a/tests/test_strelka_bp.yml +++ b/tests/test_strelka_bp.yml @@ -89,27 +89,17 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with Strelka BP without intervals @@ -210,22 +200,14 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test diff --git a/tests/test_tiddit.yml b/tests/test_tiddit.yml index 8d0c5b718c..7d397e08a4 100644 --- a/tests/test_tiddit.yml +++ b/tests/test_tiddit.yml @@ -45,27 +45,17 @@ - path: results/tiddit should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on germline sample with tiddit @@ -95,15 +85,10 @@ - path: results/tiddit should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on tumor_only sample with tiddit command: nextflow run main.nf -profile test,tools_tumoronly --tools tiddit --outdir results @@ -132,13 +117,8 @@ - path: results/tiddit should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml index 23b005ac7a..fe1642b3c3 100644 --- a/tests/test_tools_manually.yml +++ b/tests/test_tools_manually.yml @@ -35,27 +35,17 @@ - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_normalLogR.txt md5sum: 05418a7d814db11808172a4f57d040a1 - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with mutect2 without intervals @@ -107,23 +97,15 @@ - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.tbi # binary changes md5sums on reruns - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with mutect2 @@ -168,27 +150,17 @@ - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.tbi # binary changes md5sums on reruns - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run joint calling on tumor only samples with mutect2 @@ -239,15 +211,10 @@ - path: results/variant_calling/mutect2/test/test.mutect2.vcf.gz.tbi # binary changes md5sums on reruns - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - name: Run joint calling on somatic samples with mutect2 @@ -299,39 +266,24 @@ - path: results/variant_calling/mutect2/test/test.mutect2.vcf.gz.tbi # binary changes md5sums on reruns - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - name: Run full pipeline on tumoronly with most tools diff --git a/tests/test_tumor_normal_pair.yml b/tests/test_tumor_normal_pair.yml index 3bb6404249..711e494ca1 100644 --- a/tests/test_tumor_normal_pair.yml +++ b/tests/test_tumor_normal_pair.yml @@ -39,45 +39,25 @@ - path: results/reports/markduplicates/test2/test2.md.cram.metrics contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 76fa71922a3f748e507c2364c531dfcb - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: abc5df85e302b79985627888870882da - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: d536456436eb275159b8c6af83213d80 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 16cda2fae13c766a7f241600966343f4 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 05d571f8d51ca6b1bde804d7a6d999af - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 76fa71922a3f748e507c2364c531dfcb - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: abc5df85e302b79985627888870882da - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: d536456436eb275159b8c6af83213d80 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 16cda2fae13c766a7f241600966343f4 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 05d571f8d51ca6b1bde804d7a6d999af - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt - md5sum: 2020cf6dfc7ddca020c921dd9f0549b7 - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt - md5sum: 38ff8b38c33b9231f047fea8ea830aae - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt - md5sum: 8b991358768cade225470a07cd34f573 - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz - md5sum: 880c996fce059c19c4551b11b3c6f58e - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi - md5sum: eba5aca0b8f72759192bbdd29330278e - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt - md5sum: 2020cf6dfc7ddca020c921dd9f0549b7 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt - md5sum: 38ff8b38c33b9231f047fea8ea830aae - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt - md5sum: 8b991358768cade225470a07cd34f573 - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz - md5sum: 880c996fce059c19c4551b11b3c6f58e - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi - md5sum: eba5aca0b8f72759192bbdd29330278e - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_umi.yml b/tests/test_umi.yml index 69d8cf2433..0c8392f40e 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -27,25 +27,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 0 2804 3 4 0 77 0 0.027461 50115", "1.0 1 2651 2651", "12.0 8.9868 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 09d22913aa50a0207f97a3f85b182c6e - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 9359ba1c4e09aa47cc95c9134f526675 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 9bbea5e4d213a51f501c2aadff8d4526 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: ef4426cd1d433464004bb39d483abad9 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: d0713716f63ac573f4a3385733e9a537 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 09d22913aa50a0207f97a3f85b182c6e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 9359ba1c4e09aa47cc95c9134f526675 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 9bbea5e4d213a51f501c2aadff8d4526 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: ef4426cd1d433464004bb39d483abad9 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: d0713716f63ac573f4a3385733e9a537 - path: results/reports/samtools/test/test.md.cram.stats # text-based file changes md5sums on reruns - path: results/reports/samtools/test/test.recal.cram.stats From 5f2dc64f5c7bbf37cb841ddc9bea983daff730c1 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Sat, 4 May 2024 12:59:42 +0200 Subject: [PATCH 61/72] Apply suggestions from code review --- tests/test_gatk4spark.yml | 1 + tests/test_prepare_recalibration_from_bam.yml | 1 + tests/test_prepare_recalibration_from_cram.yml | 4 ++++ tests/test_recalibrate_from_bam.yml | 4 ++++ tests/test_recalibrate_from_cram.yml | 4 ++++ 5 files changed, 14 insertions(+) diff --git a/tests/test_gatk4spark.yml b/tests/test_gatk4spark.yml index 223c5699a4..cdb2cf3292 100644 --- a/tests/test_gatk4spark.yml +++ b/tests/test_gatk4spark.yml @@ -69,6 +69,7 @@ - path: results/reports/markduplicates should_exist: false - path: results/reports/mosdepth + should_exist: false - path: results/reports/samtools should_exist: false - name: Run save_output_as_bam with gatk4 spark diff --git a/tests/test_prepare_recalibration_from_bam.yml b/tests/test_prepare_recalibration_from_bam.yml index 7095fe98a0..335a67deed 100644 --- a/tests/test_prepare_recalibration_from_bam.yml +++ b/tests/test_prepare_recalibration_from_bam.yml @@ -70,6 +70,7 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth + should_exist: false - path: results/reports/samtools_stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_prepare_recalibration_from_cram.yml b/tests/test_prepare_recalibration_from_cram.yml index c002b299c3..6e362ccd7b 100644 --- a/tests/test_prepare_recalibration_from_cram.yml +++ b/tests/test_prepare_recalibration_from_cram.yml @@ -64,9 +64,13 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + should_exist: false - path: results/reports/samtools/test/test.recal.cram.stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_recalibrate_from_bam.yml b/tests/test_recalibrate_from_bam.yml index 4edc5161dd..fb96a3d305 100644 --- a/tests/test_recalibrate_from_bam.yml +++ b/tests/test_recalibrate_from_bam.yml @@ -67,9 +67,13 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + should_exist: false - path: results/reports/samtools/test/test.recal.cram.stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_recalibrate_from_cram.yml b/tests/test_recalibrate_from_cram.yml index 779fbb148f..9e53da4f2d 100644 --- a/tests/test_recalibrate_from_cram.yml +++ b/tests/test_recalibrate_from_cram.yml @@ -63,9 +63,13 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + should_exist: false - path: results/reports/samtools/test/test.recal.cram.stats should_exist: false - path: results/preprocessing/mapped/ From 5e549bfb7f2ea420a5291bead370e80a5fb235aa Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Sun, 5 May 2024 21:24:46 +0000 Subject: [PATCH 62/72] fix: remove string none option from params.ascat_genome --- CHANGELOG.md | 1 + nextflow_schema.json | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f9c03e477e..63944eaf64 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,6 +31,7 @@ Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is - [#1496](https://github.com/nf-core/sarek/pull/1496) - Fix multiple DOI handling in manifest - [#1499](https://github.com/nf-core/sarek/pull/1499) - Remove all md5sum for mosdepth tests - [#1499](https://github.com/nf-core/sarek/pull/1499) - Add mosdepth dependency to all tests runnning it +- [#1501](https://github.com/nf-core/sarek/pull/1501) - Remove string "None" param option from ascat_genome ### Removed diff --git a/nextflow_schema.json b/nextflow_schema.json index 0c58c57655..7545b9930e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -576,7 +576,7 @@ "fa_icon": "fa-solid fa-text", "description": "ASCAT genome.", "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\n\nMust be set to run ASCAT, either hg19 or hg38. If you use AWS iGenomes, this has already been set for you appropriately.", - "enum": ["None", "hg19", "hg38"], + "enum": ["hg19", "hg38"], "hidden": true }, "ascat_alleles": { From 8ff6b3dbbcf05d244fea0d6016c8c3c05a32f64b Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 6 May 2024 10:36:09 +0200 Subject: [PATCH 63/72] Update nextflow.config --- nextflow.config | 1 - 1 file changed, 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 0cd71cd319..f26930b9d1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -269,7 +269,6 @@ profiles { includeConfig 'conf/test.config' params.sentieon_dnascope_model = "az://igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model" } - test_cache { includeConfig 'conf/test/cache.config' } // Extra test profiles for full tests on AWS test_full { includeConfig 'conf/test_full.config' } test_full_aws { From da72de0c70b3ad0bc91599475374ff18224f7949 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Mon, 6 May 2024 17:29:08 -0700 Subject: [PATCH 64/72] Update CITATIONS.md with fgbio --- CITATIONS.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CITATIONS.md b/CITATIONS.md index 632a65b795..f72966d98c 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -70,6 +70,8 @@ - [FGBio](https://github.com/fulcrumgenomics/fgbio) + > doi: 10.5281/zenodo.10456900 + - [FreeBayes](https://arxiv.org/abs/1207.3907) > Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012. doi: 10.48550/arXiv.1207.3907 From 4bbc7c29469005d268ce6411b35d63fcc3f54385 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Mon, 6 May 2024 22:57:41 -0700 Subject: [PATCH 65/72] fix(TYPO): index_alignement should be index_alignment --- main.nf | 4 ++-- workflows/sarek/main.nf | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/main.nf b/main.nf index 93f896d6b9..9c272624fb 100755 --- a/main.nf +++ b/main.nf @@ -162,7 +162,7 @@ workflow NFCORE_SAREK { : PREPARE_GENOME.out.hashtable // Gather index for mapping given the chosen aligner - index_alignement = (aligner == "bwa-mem" || aligner == "sentieon-bwamem") ? bwa : + index_alignment = (aligner == "bwa-mem" || aligner == "sentieon-bwamem") ? bwa : aligner == "bwa-mem2" ? bwamem2 : dragmap @@ -279,7 +279,7 @@ workflow NFCORE_SAREK { gc_file, germline_resource, germline_resource_tbi, - index_alignement, + index_alignment, intervals_and_num_intervals, intervals_bed_combined, intervals_bed_combined_for_variant_calling, diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf index d28aabff4c..164a44f45e 100644 --- a/workflows/sarek/main.nf +++ b/workflows/sarek/main.nf @@ -106,7 +106,7 @@ workflow SAREK { gc_file germline_resource germline_resource_tbi - index_alignement + index_alignment intervals_and_num_intervals intervals_bed_combined intervals_bed_combined_for_variant_calling @@ -188,7 +188,7 @@ workflow SAREK { input_fastq, fasta, fasta_fai, - index_alignement, + index_alignment, params.group_by_umi_strategy) bam_converted_from_fastq = FASTQ_CREATE_UMI_CONSENSUS_FGBIO.out.consensusbam.map{ meta, bam -> [ meta, bam, [] ] } @@ -255,7 +255,7 @@ workflow SAREK { // reads will be sorted sort_bam = true - FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON(reads_for_alignment, index_alignement, sort_bam, fasta, fasta_fai) + FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON(reads_for_alignment, index_alignment, sort_bam, fasta, fasta_fai) // Grouping the bams from the same samples not to stall the workflow // Use groupKey to make sure that the correct group can advance as soon as it is complete From 5773d744a4b953354719318a264ec3dd431979cc Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 7 May 2024 10:43:58 +0200 Subject: [PATCH 66/72] Update README.md Adding an important comtributor --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 460f333b73..2adce0fbf8 100644 --- a/README.md +++ b/README.md @@ -169,6 +169,7 @@ We thank the following people for their extensive assistance in the development - [Sam Minot](https://github.com/sminot) - [Sebastian-D](https://github.com/Sebastian-D) - [Silvia Morini](https://github.com/silviamorins) +- [Simon Pearce](https://github.com/SPPearce) - [Solenne Correard](https://github.com/scorreard) - [Susanne Jodoin](https://github.com/SusiJo) - [Szilveszter Juhos](https://github.com/szilvajuhos) From d1f5820e72f63d01c27003d5552276cbfc9aadef Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 7 May 2024 10:45:27 +0200 Subject: [PATCH 67/72] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 63944eaf64..3cadd914f5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,7 @@ Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is - [#1485](https://github.com/nf-core/sarek/pull/1485) - Update citation for publication - [#1487](https://github.com/nf-core/sarek/pull/1487) - Update sentieon-modules to Sentieon `202308.02` - [#1490](https://github.com/nf-core/sarek/pull/1490) - Update mosdepth to `0.3.8` +- [#1509](https://github.com/nf-core/sarek/pull/1509) - Update contributors ### Fixed From 66d6e9cb04413a1aac762f3806ee8eb59a0c2f22 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 7 May 2024 10:47:48 +0200 Subject: [PATCH 68/72] Update README.md add another contributor --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 2adce0fbf8..571434f4d9 100644 --- a/README.md +++ b/README.md @@ -153,6 +153,7 @@ We thank the following people for their extensive assistance in the development - [Johannes Alneberg](https://github.com/alneberg) - [José Fernández Navarro](https://github.com/jfnavarro) - [Júlia Mir Pedrol](https://github.com/mirpedrol) +- [Ken Brewer](https://github.com/kenibrewer) - [Lasse Westergaard Folkersen](https://github.com/lassefolkersen) - [Lucia Conde](https://github.com/lconde-ucl) - [Malin Larsson](https://github.com/malinlarsson) From a2c39044fe0b5a4b37a8c2b0559547d47c01d29e Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 7 May 2024 10:57:01 +0200 Subject: [PATCH 69/72] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 63944eaf64..b770fd13fe 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,7 @@ Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is - [#1485](https://github.com/nf-core/sarek/pull/1485) - Update citation for publication - [#1487](https://github.com/nf-core/sarek/pull/1487) - Update sentieon-modules to Sentieon `202308.02` - [#1490](https://github.com/nf-core/sarek/pull/1490) - Update mosdepth to `0.3.8` +- [#1505](https://github.com/nf-core/sarek/pull/1505) - Update CITATIONS.md ### Fixed From 6eb89435e8639a188ebe8b124715a5766962a0ad Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 7 May 2024 11:00:09 +0200 Subject: [PATCH 70/72] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 63944eaf64..b96762f898 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,7 @@ Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is - [#1485](https://github.com/nf-core/sarek/pull/1485) - Update citation for publication - [#1487](https://github.com/nf-core/sarek/pull/1487) - Update sentieon-modules to Sentieon `202308.02` - [#1490](https://github.com/nf-core/sarek/pull/1490) - Update mosdepth to `0.3.8` +- [#1506](https://github.com/nf-core/sarek/pull/1506) - Fixing typos (`index_alignement` -> `index_alignment`) ### Fixed From 8e87fcbc9ed033a069cdc77b42c5b686e329617e Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 7 May 2024 11:02:05 +0200 Subject: [PATCH 71/72] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 571434f4d9..61e7e158ea 100644 --- a/README.md +++ b/README.md @@ -161,6 +161,7 @@ We thank the following people for their extensive assistance in the development - [Nick Smith](https://github.com/nickhsmith) - [Nicolas Schcolnicov](https://github.com/nschcolnicov) - [Nilesh Tawari](https://github.com/nilesh-tawari) +- [Nils Homer](https://github.com/nh13) - [Olga Botvinnik](https://github.com/olgabot) - [Oskar Wacker](https://github.com/WackerO) - [pallolason](https://github.com/pallolason) From 552d04991ab1408c8e56b7ca21b7a60b9bf2aa1b Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 7 May 2024 12:13:55 +0200 Subject: [PATCH 72/72] Apply suggestions from code review Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- CHANGELOG.md | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index be452a300c..4257960df7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [3.4.2](https://github.com/nf-core/sarek/releases/tag/3.4.2) - Sájtáristjåhkkå -Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is one of the few peak in Sweden that cannot be climbed without proper climbing equipments. +Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is one of the few peaks in Sweden that cannot be climbed without proper climbing equipment. ### Added diff --git a/README.md b/README.md index 61e7e158ea..490230d700 100644 --- a/README.md +++ b/README.md @@ -196,7 +196,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# If you use `nf-core/sarek` for your analysis, please cite the `Sarek` article as follows: -> Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven Nahnsen **Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery** _ NAR Genomics and Bioinformatics_ Volume 6, Issue 2, June 2024, lqae031, [doi: 10.1093/nargab/lqae031](https://doi.org/10.1093/nargab/lqae031). +> Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven Nahnsen **Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery** _NAR Genomics and Bioinformatics_ Volume 6, Issue 2, June 2024, lqae031, [doi: 10.1093/nargab/lqae031](https://doi.org/10.1093/nargab/lqae031). > Garcia M, Juhos S, Larsson M et al. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved]** _F1000Research_ 2020, 9:63 [doi: 10.12688/f1000research.16665.2](http://dx.doi.org/10.12688/f1000research.16665.2).