From febbcff77ed35113dac3eeb0615460559d0565b1 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Wed, 20 Sep 2023 11:31:07 +0100 Subject: [PATCH 01/21] nf-core lint --fix files_unchanged ( nf-core 2.8) --- .github/workflows/linting.yml | 2 +- lib/NfcoreSchema.groovy | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 858d622..888cb4b 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.7" + python-version: "3.8" architecture: "x64" - name: Install dependencies diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy index 33cd4f6..9b34804 100755 --- a/lib/NfcoreSchema.groovy +++ b/lib/NfcoreSchema.groovy @@ -2,6 +2,7 @@ // This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. // +import nextflow.Nextflow import org.everit.json.schema.Schema import org.everit.json.schema.loader.SchemaLoader import org.everit.json.schema.ValidationException @@ -83,6 +84,7 @@ class NfcoreSchema { 'stub-run', 'test', 'w', + 'with-apptainer', 'with-charliecloud', 'with-conda', 'with-dag', @@ -177,7 +179,7 @@ class NfcoreSchema { } if (has_error) { - System.exit(1) + Nextflow.error('Exiting!') } } From 5fc66d604e6affd030878532ae8818357ddf6419 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Wed, 20 Sep 2023 11:33:28 +0100 Subject: [PATCH 02/21] nf-core modules update bcftools/concat --- modules.json | 2 +- modules/nf-core/bcftools/concat/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules.json b/modules.json index 5ab5a99..e3332ee 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "bcftools/concat": { "branch": "master", - "git_sha": "fa12afdf5874c1d11e4a20efe81c97935e8eea24", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "cat/cat": { diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index de9ba67..244a42c 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_CONCAT { conda "bioconda::bcftools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0': - 'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }" + 'biocontainers/bcftools:1.17--haef29d1_0' }" input: tuple val(meta), path(vcfs), path(tbi) From 3c7c11ae1a65fa344658dd560f85e78abd097b39 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Wed, 20 Sep 2023 11:34:23 +0100 Subject: [PATCH 03/21] nf-core modules update cat/cat --- modules.json | 2 +- modules/nf-core/cat/cat/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules.json b/modules.json index e3332ee..7aa08b7 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "cat/cat": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 840af4b..9f06221 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -5,7 +5,7 @@ process CAT_CAT { conda "conda-forge::pigz=2.3.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : - 'quay.io/biocontainers/pigz:2.3.4' }" + 'biocontainers/pigz:2.3.4' }" input: tuple val(meta), path(files_in) From bed22982c36481de35e7f52dd58f545df661e1c2 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Wed, 20 Sep 2023 11:36:39 +0100 Subject: [PATCH 04/21] nf-core modules update custom/dumpsoftwareversions --- modules.json | 2 +- modules/nf-core/custom/dumpsoftwareversions/main.nf | 6 +++--- modules/nf-core/custom/dumpsoftwareversions/meta.yml | 2 ++ .../dumpsoftwareversions/templates/dumpsoftwareversions.py | 0 4 files changed, 6 insertions(+), 4 deletions(-) mode change 100644 => 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py diff --git a/modules.json b/modules.json index 7aa08b7..24c99bd 100644 --- a/modules.json +++ b/modules.json @@ -17,7 +17,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "7101db4432d3268b7fcb5b8f75fa0a022dc5561b", + "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", "installed_by": ["modules"] }, "deepvariant": { diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 800a609..c9d014b 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index 60b546a..c32657d 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,7 +1,9 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: - custom + - dump - version tools: - custom: diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py old mode 100644 new mode 100755 From c9b4e23fc2abbc4f905a135b18f0e1d47c5609b8 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Wed, 20 Sep 2023 13:38:15 +0100 Subject: [PATCH 05/21] nf-core modules update deepvariant --- modules.json | 5 ++-- modules/nf-core/deepvariant/main.nf | 36 +++++++++++++++++----------- modules/nf-core/deepvariant/meta.yml | 17 +++++++++++++ 3 files changed, 41 insertions(+), 17 deletions(-) diff --git a/modules.json b/modules.json index 24c99bd..297798d 100644 --- a/modules.json +++ b/modules.json @@ -22,9 +22,8 @@ }, "deepvariant": { "branch": "master", - "git_sha": "58b5e78506e66f7ecd610fa825890ed9fb98b793", - "installed_by": ["modules"], - "patch": "modules/nf-core/deepvariant/deepvariant.diff" + "git_sha": "ed67f2fadd6d2a155b296f728e6b1f8c92ddc1a6", + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf index 434fcc0..2d5c480 100644 --- a/modules/nf-core/deepvariant/main.nf +++ b/modules/nf-core/deepvariant/main.nf @@ -1,32 +1,33 @@ process DEEPVARIANT { tag "$meta.id" - label 'process_medium' + label 'process_high' - container "google/deepvariant:1.4.0" - - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." - } + container "nf-core/deepvariant:1.5.0" input: tuple val(meta), path(input), path(index), path(intervals) - path(fasta) - path(fai) - path(gzi) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(gzi) output: - tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf - tuple val(meta), path("${prefix}.g.vcf.gz"), emit: gvcf - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf + tuple val(meta), path("${prefix}.vcf.gz.tbi") , emit: vcf_tbi + tuple val(meta), path("${prefix}.g.vcf.gz") , emit: gvcf + tuple val(meta), path("${prefix}.g.vcf.gz.tbi"), emit: gvcf_tbi + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" - def regions = intervals ? "--regions ${intervals}" : "" + def regions = intervals ? "--regions=${intervals}" : "" """ /opt/deepvariant/bin/run_deepvariant \\ @@ -36,6 +37,7 @@ process DEEPVARIANT { --output_gvcf=${prefix}.g.vcf.gz \\ ${args} \\ ${regions} \\ + --intermediate_results_dir=. \\ --num_shards=${task.cpus} cat <<-END_VERSIONS > versions.yml @@ -45,10 +47,16 @@ process DEEPVARIANT { """ stub: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." + } prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi touch ${prefix}.g.vcf.gz + touch ${prefix}.g.vcf.gz.tbi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/deepvariant/meta.yml b/modules/nf-core/deepvariant/meta.yml index 63868b2..c7d11ae 100644 --- a/modules/nf-core/deepvariant/meta.yml +++ b/modules/nf-core/deepvariant/meta.yml @@ -3,6 +3,7 @@ description: DeepVariant is an analysis pipeline that uses a deep neural network keywords: - variant calling - machine learning + - neural network tools: - deepvariant: description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data @@ -30,14 +31,29 @@ input: type: file description: Interval file for targeted regions pattern: "*.bed" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - fasta: type: file description: The reference fasta file pattern: "*.fasta" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - fai: type: file description: Index of reference fasta file pattern: "*.fai" + - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - gzi: type: file description: GZI index of reference fasta file @@ -64,3 +80,4 @@ output: authors: - "@abhi18av" + - "@ramprasadn" From 77890858729c07eb0827c2a7d9c0431e67082790 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Wed, 20 Sep 2023 19:23:52 +0100 Subject: [PATCH 06/21] add pipeline template file --- pipeline_template.yml | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 pipeline_template.yml diff --git a/pipeline_template.yml b/pipeline_template.yml new file mode 100644 index 0000000..0aa7398 --- /dev/null +++ b/pipeline_template.yml @@ -0,0 +1,3 @@ +prefix: sanger-tol +skip: + - igenomes From 7a3aeb87f70f6450555a46dc8ba45fb03488a014 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Thu, 21 Sep 2023 15:10:24 +0100 Subject: [PATCH 07/21] Template update for nf-core/tools version 2.8 --- .editorconfig | 2 +- .github/CONTRIBUTING.md | 6 +- .github/ISSUE_TEMPLATE/bug_report.yml | 3 +- .github/PULL_REQUEST_TEMPLATE.md | 4 +- .github/workflows/branch.yml | 18 +-- .github/workflows/clean-up.yml | 24 ++++ .github/workflows/linting.yml | 2 +- .github/workflows/sangerfulltest.yml | 37 ----- .github/workflows/sangertest.yml | 24 ---- .nf-core.yml | 11 +- .pre-commit-config.yaml | 5 + CHANGELOG.md | 2 +- CITATIONS.md | 5 + LICENSE | 2 +- README.md | 65 +++++---- assets/email_template.html | 2 +- assets/multiqc_config.yml | 12 ++ assets/schema_input.json | 2 +- assets/sendmail_template.txt | 25 ++++ bin/check_samplesheet.py | 3 - conf/base.config | 2 +- conf/modules.config | 4 + conf/test_full.config | 2 + docs/images/mqc_fastqc_adapter.png | Bin 0 -> 23458 bytes docs/images/mqc_fastqc_counts.png | Bin 0 -> 33918 bytes docs/images/mqc_fastqc_quality.png | Bin 0 -> 55769 bytes docs/output.md | 41 +++++- docs/usage.md | 132 ++++++------------ lib/NfcoreSchema.groovy | 4 +- lib/NfcoreTemplate.groovy | 38 ++++- lib/WorkflowMain.groovy | 18 ++- lib/WorkflowVariantcalling.groovy | 49 ++++++- main.nf | 3 +- modules.json | 12 +- modules/local/samplesheet_check.nf | 2 +- .../custom/dumpsoftwareversions/meta.yml | 2 + .../templates/dumpsoftwareversions.py | 3 +- modules/nf-core/fastqc/main.nf | 51 +++++++ modules/nf-core/fastqc/meta.yml | 52 +++++++ modules/nf-core/multiqc/main.nf | 53 +++++++ modules/nf-core/multiqc/meta.yml | 56 ++++++++ nextflow.config | 44 +++++- nextflow_schema.json | 34 ++++- pipeline_template.yml | 2 +- tower.yml | 5 + workflows/variantcalling.nf | 42 +++++- 46 files changed, 663 insertions(+), 242 deletions(-) create mode 100644 .github/workflows/clean-up.yml delete mode 100644 .github/workflows/sangerfulltest.yml delete mode 100644 .github/workflows/sangertest.yml create mode 100644 .pre-commit-config.yaml create mode 100644 assets/multiqc_config.yml create mode 100755 docs/images/mqc_fastqc_adapter.png create mode 100755 docs/images/mqc_fastqc_counts.png create mode 100755 docs/images/mqc_fastqc_quality.png create mode 100644 modules/nf-core/fastqc/main.nf create mode 100644 modules/nf-core/fastqc/meta.yml create mode 100644 modules/nf-core/multiqc/main.nf create mode 100644 modules/nf-core/multiqc/meta.yml create mode 100644 tower.yml diff --git a/.editorconfig b/.editorconfig index b78de6e..b6b3190 100644 --- a/.editorconfig +++ b/.editorconfig @@ -8,7 +8,7 @@ trim_trailing_whitespace = true indent_size = 4 indent_style = space -[*.{md,yml,yaml,html,css,scss,js,cff}] +[*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 # These files are edited and tested upstream in nf-core/modules diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 61c8548..fb9e100 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -46,9 +46,9 @@ These tests are run both with the latest available version of `Nextflow` and als :warning: Only in the unlikely and regretful event of a release happening with a bug. -- On your own fork, make a new branch `patch` based on `upstream/main`. +- On your own fork, make a new branch `patch` based on `upstream/master`. - Fix the bug, and bump version (X.Y.Z+1). -- A PR should be made on `main` from patch to directly this particular bug. +- A PR should be made on `master` from patch to directly this particular bug. ## Pipeline contribution conventions @@ -66,6 +66,8 @@ If you wish to contribute a new step, please use the following coding standards: 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. +9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. +10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. ### Default values diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index fa96bcf..1df5965 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -44,7 +44,8 @@ body: * Executor _(eg. slurm, local, awsbatch)_ - * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_ + * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, + or Apptainer)_ * OS _(eg. CentOS Linux, macOS, Linux Mint)_ diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 23d7977..d8affa1 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. -Learn more about contributing: [CONTRIBUTING.md](https://github.com/sanger-tol/variantcalling/tree/main/.github/CONTRIBUTING.md) +Learn more about contributing: [CONTRIBUTING.md](https://github.com/sanger-tol/variantcalling/tree/master/.github/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/sanger-tol/variantcalling/tree/main/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/sanger-tol/variantcalling/tree/master/.github/CONTRIBUTING.md) - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index bd3eccf..5defeb5 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -1,19 +1,19 @@ name: nf-core branch protection -# This workflow is triggered on PRs to main branch on the repository -# It fails when someone tries to make a PR against the nf-core `main` branch instead of `dev` +# This workflow is triggered on PRs to master branch on the repository +# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` on: pull_request_target: - branches: [main] + branches: [master] jobs: test: runs-on: ubuntu-latest steps: - # PRs to the nf-core repo main branch are only ok if coming from the nf-core repo `dev` or any `patch` branches + # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches - name: Check PRs if: github.repository == 'sanger-tol/variantcalling' run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == sanger-tol/variantcalling ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ ${{github.event.pull_request.head.repo.full_name }} == sanger-tol/variantcalling ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets @@ -22,7 +22,7 @@ jobs: uses: mshick/add-pr-comment@v1 with: message: | - ## This PR is against the `main` branch :x: + ## This PR is against the `master` branch :x: * Do not close this PR * Click _Edit_ and change the `base` to `dev` @@ -32,9 +32,9 @@ jobs: Hi @${{ github.event.pull_request.user.login }}, - It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `main` branch. - The `main` branch on nf-core repositories should always contain code from the latest release. - Because of this, PRs to `main` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. + It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. + The `master` branch on nf-core repositories should always contain code from the latest release. + Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit. diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml new file mode 100644 index 0000000..694e90e --- /dev/null +++ b/.github/workflows/clean-up.yml @@ -0,0 +1,24 @@ +name: "Close user-tagged issues and PRs" +on: + schedule: + - cron: "0 0 * * 0" # Once a week + +jobs: + clean-up: + runs-on: ubuntu-latest + permissions: + issues: write + pull-requests: write + steps: + - uses: actions/stale@v7 + with: + stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." + stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." + close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." + days-before-stale: 30 + days-before-close: 20 + days-before-pr-close: -1 + any-of-labels: "awaiting-changes,awaiting-feedback" + exempt-issue-labels: "WIP" + exempt-pr-labels: "WIP" + repo-token: "${{ secrets.GITHUB_TOKEN }}" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 858d622..888cb4b 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.7" + python-version: "3.8" architecture: "x64" - name: Install dependencies diff --git a/.github/workflows/sangerfulltest.yml b/.github/workflows/sangerfulltest.yml deleted file mode 100644 index 9d266be..0000000 --- a/.github/workflows/sangerfulltest.yml +++ /dev/null @@ -1,37 +0,0 @@ -name: sanger-tol LSF full size tests - -on: - push: - branches: - - main - - dev - workflow_dispatch: -jobs: - run-tower: - name: Run LSF full size tests - runs-on: ubuntu-latest - steps: - - name: Sets env vars for push - run: | - echo "REVISION=${{ github.sha }}" >> $GITHUB_ENV - if: github.event_name == 'push' - - - name: Sets env vars for workflow_dispatch - run: | - echo "REVISION=${{ github.sha }}" >> $GITHUB_ENV - if: github.event_name == 'workflow_dispatch' - - - name: Launch workflow via tower - uses: nf-core/tower-action@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - pipeline: ${{ github.repository }} - revision: ${{ env.REVISION }} - workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ env.REVISION }} - parameters: | - { - "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}", - } - profiles: test_full,sanger,singularity diff --git a/.github/workflows/sangertest.yml b/.github/workflows/sangertest.yml deleted file mode 100644 index f1395fa..0000000 --- a/.github/workflows/sangertest.yml +++ /dev/null @@ -1,24 +0,0 @@ -name: sanger-tol LSF tests - -on: - workflow_dispatch: - -jobs: - run-tower: - name: Run LSF tests - runs-on: ubuntu-latest - steps: - - name: Launch workflow via tower - uses: nf-core/tower-action@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - pipeline: ${{ github.repository }} - revision: ${{ github.sha }} - workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ github.sha }} - parameters: | - { - "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ github.sha }}", - } - profiles: test,sanger,singularity diff --git a/.nf-core.yml b/.nf-core.yml index 9caa7b0..3de0af8 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -8,15 +8,8 @@ lint: - .github/ISSUE_TEMPLATE/config.yml - .github/workflows/awstest.yml - .github/workflows/awsfulltest.yml - - assets/multiqc_config.yml - - conf/igenomes.config - files_unchanged: - - .github/CONTRIBUTING.md - - assets/sendmail_template.txt - - lib/NfcoreTemplate.groovy - - .github/PULL_REQUEST_TEMPLATE.md - - .github/workflows/branch.yml - nextflow_config: - manifest.name - manifest.homePage + multiqc_config: + - report_comment diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..0c31cdb --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,5 @@ +repos: + - repo: https://github.com/pre-commit/mirrors-prettier + rev: "v2.7.1" + hooks: + - id: prettier diff --git a/CHANGELOG.md b/CHANGELOG.md index c290a15..84a9bdc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0dev - [date] +## v1.0.0 - [date] Initial release of sanger-tol/variantcalling, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index 4abdbdc..0d722f8 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,6 +10,11 @@ ## Pipeline tools +- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) + +- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + ## Software packaging/containerisation tools - [Anaconda](https://anaconda.com) diff --git a/LICENSE b/LICENSE index 7e408f7..f5f150c 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) Guoying Qi +Copyright (c) @muffato, @gq1, @priyanka-surana Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index fc0cdd2..6efa459 100644 --- a/README.md +++ b/README.md @@ -8,50 +8,63 @@ ## Introduction - +**sanger-tol/variantcalling** is a bioinformatics pipeline that ... -**sanger-tol/variantcalling** is a bioinformatics best-practice analysis pipeline for variant calling. + -The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! - - + + -On release, automated continuous integration tests run the pipeline on a full-sized dataset on the LSF infrastructure. This ensures that the pipeline runs on LSF, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. +1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) +2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) -## Pipeline summary +## Usage - +> **Note** +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) +> with `-profile test` before running the workflow on actual data. -## Quick Start + - > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. - > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. - > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. +Now, you can run the pipeline using: -4. Start running your own analysis! + - +```bash +nextflow run sanger-tol/variantcalling \ + -profile \ + --input samplesheet.csv \ + --outdir +``` - ```bash - nextflow run sanger-tol/variantcalling --input samplesheet.csv --outdir --genome GRCh37 -profile - ``` +> **Warning:** +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those +> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; +> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). ## Credits -sanger-tol/variantcalling was originally written by Guoying Qi. +sanger-tol/variantcalling was originally written by @muffato, @gq1, @priyanka-surana. We thank the following people for their extensive assistance in the development of this pipeline: diff --git a/assets/email_template.html b/assets/email_template.html index 68aa3d4..7bf2fb1 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -4,7 +4,7 @@ - + sanger-tol/variantcalling Pipeline Report diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml new file mode 100644 index 0000000..34e2778 --- /dev/null +++ b/assets/multiqc_config.yml @@ -0,0 +1,12 @@ +report_comment: > + This report has been generated by the sanger-tol/variantcalling + analysis pipeline. +report_section_order: + "sanger-tol-variantcalling-methods-description": + order: -1000 + software_versions: + order: -1001 + "sanger-tol-variantcalling-summary": + order: -1002 + +export_plots: true diff --git a/assets/schema_input.json b/assets/schema_input.json index 50f9182..f97020b 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,6 +1,6 @@ { "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/sanger-tol/variantcalling/main/assets/schema_input.json", + "$id": "https://raw.githubusercontent.com/sanger-tol/variantcalling/master/assets/schema_input.json", "title": "sanger-tol/variantcalling pipeline - params.input schema", "description": "Schema for the file provided with params.input", "type": "array", diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt index 4ba6479..5e43653 100644 --- a/assets/sendmail_template.txt +++ b/assets/sendmail_template.txt @@ -25,4 +25,29 @@ Content-Disposition: inline; filename="sanger-tol-variantcalling_logo_light.png" flatten(). join( '\n' ) %> +<% +if (mqcFile){ +def mqcFileObj = new File("$mqcFile") +if (mqcFileObj.length() < mqcMaxSize){ +out << """ +--nfcoremimeboundary +Content-Type: text/html; name=\"multiqc_report\" +Content-Transfer-Encoding: base64 +Content-ID: +Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\" + +${mqcFileObj. + bytes. + encodeBase64(). + toString(). + tokenize( '\n' )*. + toList()*. + collate( 76 )*. + collect { it.join() }. + flatten(). + join( '\n' )} +""" +}} +%> + --nfcoremimeboundary-- diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 11b1557..4a758fe 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -158,9 +158,6 @@ def sniff_format(handle): peek = read_head(handle) handle.seek(0) sniffer = csv.Sniffer() - if not sniffer.has_header(peek): - logger.critical("The given sample sheet does not appear to contain a header.") - sys.exit(1) dialect = sniffer.sniff(peek) return dialect diff --git a/conf/base.config b/conf/base.config index df5f785..f43592d 100644 --- a/conf/base.config +++ b/conf/base.config @@ -15,7 +15,7 @@ process { memory = { check_max( 6.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } - errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' diff --git a/conf/modules.config b/conf/modules.config index 60f6467..da58a5d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -26,6 +26,10 @@ process { ] } + withName: FASTQC { + ext.args = '--quiet' + } + withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ path: { "${params.outdir}/pipeline_info" }, diff --git a/conf/test_full.config b/conf/test_full.config index ac21d74..9f207b2 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,6 +10,8 @@ ---------------------------------------------------------------------------------------- */ +cleanup = true + params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png new file mode 100755 index 0000000000000000000000000000000000000000..361d0e47acfb424dea1f326590d1eb2f6dfa26b5 GIT binary patch literal 23458 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zXwhtT%ei{n#FzEH|C;yZ>+$!u_x#*+`=L8{b9SH^9&27u3G_Gxqxe`L2UJtdxghk z&-wzDFvLvW{chK5u3{n6GSKKy!P&C6w^IFpbD0bcp^A{{2lcLh_DXj@ybtYvc^;(2 M)78&qol`;+0Fu7JivR!s literal 0 HcmV?d00001 diff --git a/docs/output.md b/docs/output.md index 07a9d89..3666250 100644 --- a/docs/output.md +++ b/docs/output.md @@ -2,7 +2,7 @@ ## Introduction -This document describes the output produced by the pipeline. +This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline. The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. @@ -12,8 +12,47 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: +- [FastQC](#fastqc) - Raw read QC +- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution +### FastQC + +
+Output files + +- `fastqc/` + - `*_fastqc.html`: FastQC report containing quality metrics. + - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. + +
+ +[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). + +![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) + +![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) + +![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) + +> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. + +### MultiQC + +
+Output files + +- `multiqc/` + - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. + - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. + - `multiqc_plots/`: directory containing static images from the report in various formats. + +
+ +[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. + +Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . + ### Pipeline information
diff --git a/docs/usage.md b/docs/usage.md index d337109..ff01839 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -69,6 +69,29 @@ work # Directory containing the nextflow working files # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` +If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file. + +Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. + +> ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). +> The above pipeline run specified with a params file in yaml format: + +```bash +nextflow run sanger-tol/variantcalling -profile docker -params-file params.yaml +``` + +with `params.yaml` containing: + +```yaml +input: './samplesheet.csv' +outdir: './results/' +genome: 'GRCh37' +input: 'data' +<...> +``` + +You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). + ### Updating the pipeline When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: @@ -83,7 +106,11 @@ It is a good idea to specify a pipeline version when running the pipeline on you First, go to the [sanger-tol/variantcalling releases page](https://github.com/sanger-tol/variantcalling/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. -This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. +This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. + +To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. + +> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. ## Core Nextflow arguments @@ -93,7 +120,7 @@ This version number will be logged in reports when you run the pipeline, so that Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. -Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. +Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. @@ -117,8 +144,10 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) - `charliecloud` - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) +- `apptainer` + - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `conda` - - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. + - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. ### `-resume` @@ -136,102 +165,19 @@ Specify the path to a specific config file (this is a core Nextflow command). Se Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. -For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue: - -```console -[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1) -Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)' - -Caused by: - Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) - -Command executed: - STAR \ - --genomeDir star \ - --readFilesIn WT_REP1_trimmed.fq.gz \ - --runThreadN 2 \ - --outFileNamePrefix WT_REP1. \ - - -Command exit status: - 137 - -Command output: - (empty) - -Command error: - .command.sh: line 9: 30 Killed STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. -Work dir: - /home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb - -Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` -``` - -#### For beginners - -A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters `--max_cpus`, `--max_memory`, and `--max_time`. Based on the error above, you have to increase the amount of memory. Therefore you can go to the [parameter documentation of rnaseq](https://nf-co.re/rnaseq/3.9/parameters) and scroll down to the `show hidden parameter` button to get the default value for `--max_memory`. In this case 128GB, you than can try to run your pipeline again with `--max_memory 200GB -resume` to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below. - -#### Advanced option on process level - -To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). -We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/star/align/main.nf`. -If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). -The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. -The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. -Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. -The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections. - -```nextflow -process { - withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' { - memory = 100.GB - } -} -``` - -> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden. -> -> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. - -### Updating containers (advanced users) - -The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`. - -1. Check the default version used by the pipeline in the module file for [Pangolin](https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/modules/nf-core/software/pangolin/main.nf#L14-L19) -2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags) -3. Create the custom config accordingly: - - - For Docker: +To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. - ```nextflow - process { - withName: PANGOLIN { - container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` +### Custom Containers - - For Singularity: +In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. - ```nextflow - process { - withName: PANGOLIN { - container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` +To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. - - For Conda: +### Custom Tool Arguments - ```nextflow - process { - withName: PANGOLIN { - conda = 'bioconda::pangolin=3.0.5' - } - } - ``` +A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. -> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch. +To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. ### nf-core/configs diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy index 33cd4f6..9b34804 100755 --- a/lib/NfcoreSchema.groovy +++ b/lib/NfcoreSchema.groovy @@ -2,6 +2,7 @@ // This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. // +import nextflow.Nextflow import org.everit.json.schema.Schema import org.everit.json.schema.loader.SchemaLoader import org.everit.json.schema.ValidationException @@ -83,6 +84,7 @@ class NfcoreSchema { 'stub-run', 'test', 'w', + 'with-apptainer', 'with-charliecloud', 'with-conda', 'with-dag', @@ -177,7 +179,7 @@ class NfcoreSchema { } if (has_error) { - System.exit(1) + Nextflow.error('Exiting!') } } diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 6ddfe19..2023f45 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -6,6 +6,18 @@ import org.yaml.snakeyaml.Yaml class NfcoreTemplate { + // + // Check AWS Batch related parameters have been specified correctly + // + public static void awsBatch(workflow, params) { + if (workflow.profile.contains('awsbatch')) { + // Check params.awsqueue and params.awsregion have been set if running on AWSBatch + assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" + // Check outdir paths to be S3 buckets if running on AWSBatch + assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" + } + } + // // Warn if a -profile or Nextflow config has not been provided to run the pipeline // @@ -42,7 +54,7 @@ class NfcoreTemplate { // // Construct and send completion email // - public static void email(workflow, params, summary_params, projectDir, log) { + public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) { // Set up the e-mail variables def subject = "[$workflow.manifest.name] Successful: $workflow.runName" @@ -80,6 +92,24 @@ class NfcoreTemplate { email_fields['projectDir'] = workflow.projectDir email_fields['summary'] = summary << misc_fields + // On success try attach the multiqc report + def mqc_report = null + try { + if (workflow.success) { + mqc_report = multiqc_report.getVal() + if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { + if (mqc_report.size() > 1) { + log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + } + mqc_report = mqc_report[0] + } + } + } catch (all) { + if (multiqc_report) { + log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + } + } + // Check if we are only sending emails on failure def email_address = params.email if (!params.email && params.email_on_fail && !workflow.success) { @@ -98,7 +128,8 @@ class NfcoreTemplate { def email_html = html_template.toString() // Render the sendmail template - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir" ] + def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit + def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] def sf = new File("$projectDir/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_html = sendmail_template.toString() @@ -114,6 +145,9 @@ class NfcoreTemplate { } catch (all) { // Catch failures and try with plaintext def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) { + mail_cmd += [ '-A', mqc_report ] + } mail_cmd.execute() << email_html log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" } diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index a25a7d5..56ba5cb 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -2,6 +2,8 @@ // This file holds several functions specific to the main.nf workflow in the sanger-tol/variantcalling pipeline // +import nextflow.Nextflow + class WorkflowMain { // @@ -15,13 +17,13 @@ class WorkflowMain { "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/main/CITATIONS.md" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } // // Generate help string // - public static String help(workflow, params, log) { + public static String help(workflow, params) { def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --fasta reference.fa -profile docker" def help_string = '' help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) @@ -34,7 +36,7 @@ class WorkflowMain { // // Generate parameter summary log string // - public static String paramsSummaryLog(workflow, params, log) { + public static String paramsSummaryLog(workflow, params) { def summary_log = '' summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) @@ -49,7 +51,7 @@ class WorkflowMain { public static void initialise(workflow, params, log) { // Print help to screen if required if (params.help) { - log.info help(workflow, params, log) + log.info help(workflow, params) System.exit(0) } @@ -61,7 +63,7 @@ class WorkflowMain { } // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params, log) + log.info paramsSummaryLog(workflow, params) // Validate workflow parameters via the JSON schema if (params.validate_params) { @@ -76,10 +78,12 @@ class WorkflowMain { Utils.checkCondaChannels(log) } + // Check AWS batch settings + NfcoreTemplate.awsBatch(workflow, params) + // Check input has been provided if (!params.input) { - log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'" - System.exit(1) + Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") } } } diff --git a/lib/WorkflowVariantcalling.groovy b/lib/WorkflowVariantcalling.groovy index dad2c91..f64085e 100755 --- a/lib/WorkflowVariantcalling.groovy +++ b/lib/WorkflowVariantcalling.groovy @@ -2,6 +2,7 @@ // This file holds several functions specific to the workflow/variantcalling.nf in the sanger-tol/variantcalling pipeline // +import nextflow.Nextflow import groovy.text.SimpleTemplateEngine class WorkflowVariantcalling { @@ -10,11 +11,53 @@ class WorkflowVariantcalling { // Check and validate parameters // public static void initialise(params, log) { + if (!params.fasta) { - log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." - System.exit(1) + Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." } } -} + // + // Get workflow summary for MultiQC + // + public static String paramsSummaryMultiqc(workflow, summary) { + String summary_section = '' + for (group in summary.keySet()) { + def group_params = summary.get(group) // This gets the parameters of that particular group + if (group_params) { + summary_section += "

$group

\n" + summary_section += "
\n" + for (param in group_params.keySet()) { + summary_section += "
$param
${group_params.get(param) ?: 'N/A'}
\n" + } + summary_section += "
\n" + } + } + + String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" + return yaml_file_text + } + + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + def meta = [:] + meta.workflow = run_workflow.toMap() + meta["manifest_map"] = run_workflow.manifest.toMap() + + meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + + def methods_text = mqc_methods_yaml.text + + def engine = new SimpleTemplateEngine() + def description_html = engine.createTemplate(methods_text).make(meta) + + return description_html + }} diff --git a/main.nf b/main.nf index 61d8c25..7582b32 100644 --- a/main.nf +++ b/main.nf @@ -3,8 +3,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sanger-tol/variantcalling ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Github : https://github.com/sanger-tol/variantcalling ----------------------------------------------------------------------------------------- + Github : https://github.com/sanger-tol/variantcalling---------------------------------------------------------------------------------------- */ nextflow.enable.dsl = 2 diff --git a/modules.json b/modules.json index 8953ab5..4b03a7d 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,17 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "b6d4d476aee074311c89d82a69c1921bd70c8180", + "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543", + "installed_by": ["modules"] + }, + "fastqc": { + "branch": "master", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "installed_by": ["modules"] + }, + "multiqc": { + "branch": "master", + "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7", "installed_by": ["modules"] } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 264bee0..0505378 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK { conda "conda-forge::python=3.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'quay.io/biocontainers/python:3.8.3' }" + 'biocontainers/python:3.8.3' }" input: path samplesheet diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index 60b546a..c32657d 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,7 +1,9 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: - custom + - dump - version tools: - custom: diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index da03340..e55b8d4 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -4,10 +4,11 @@ """Provide functions to merge multiple versions.yml files.""" -import yaml import platform from textwrap import dedent +import yaml + def _make_versions_html(versions): """Generate a tabular HTML output of all versions for MultiQC.""" diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf new file mode 100644 index 0000000..9ae5838 --- /dev/null +++ b/modules/nf-core/fastqc/main.nf @@ -0,0 +1,51 @@ +process FASTQC { + tag "$meta.id" + label 'process_medium' + + conda "bioconda::fastqc=0.11.9" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : + 'quay.io/biocontainers/fastqc:0.11.9--0' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("*.html"), emit: html + tuple val(meta), path("*.zip") , emit: zip + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + // Make list of old name and new name pairs to use for renaming in the bash while loop + def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } + def rename_to = old_new_pairs*.join(' ').join(' ') + def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + """ + printf "%s %s\\n" $rename_to | while read old_name new_name; do + [ -f "\${new_name}" ] || ln -s \$old_name \$new_name + done + fastqc $args --threads $task.cpus $renamed_files + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.html + touch ${prefix}.zip + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml new file mode 100644 index 0000000..4da5bb5 --- /dev/null +++ b/modules/nf-core/fastqc/meta.yml @@ -0,0 +1,52 @@ +name: fastqc +description: Run FastQC on sequenced reads +keywords: + - quality control + - qc + - adapters + - fastq +tools: + - fastqc: + description: | + FastQC gives general quality metrics about your reads. + It provides information about the quality score distribution + across your reads, the per base sequence content (%A/C/G/T). + You get information about adapter contamination and other + overrepresented sequences. + homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ + licence: ["GPL-2.0-only"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - html: + type: file + description: FastQC report + pattern: "*_{fastqc.html}" + - zip: + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf new file mode 100644 index 0000000..4b60474 --- /dev/null +++ b/modules/nf-core/multiqc/main.nf @@ -0,0 +1,53 @@ +process MULTIQC { + label 'process_single' + + conda "bioconda::multiqc=1.14" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" + + input: + path multiqc_files, stageAs: "?/*" + path(multiqc_config) + path(extra_multiqc_config) + path(multiqc_logo) + + output: + path "*multiqc_report.html", emit: report + path "*_data" , emit: data + path "*_plots" , optional:true, emit: plots + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def config = multiqc_config ? "--config $multiqc_config" : '' + def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + """ + multiqc \\ + --force \\ + $args \\ + $config \\ + $extra_config \\ + . + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS + """ + + stub: + """ + touch multiqc_data + touch multiqc_plots + touch multiqc_report.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml new file mode 100644 index 0000000..f93b5ee --- /dev/null +++ b/modules/nf-core/multiqc/meta.yml @@ -0,0 +1,56 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +name: MultiQC +description: Aggregate results from bioinformatics analyses across many samples into a single report +keywords: + - QC + - bioinformatics tools + - Beautiful stand-alone HTML report +tools: + - multiqc: + description: | + MultiQC searches a given directory for analysis logs and compiles a HTML report. + It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + homepage: https://multiqc.info/ + documentation: https://multiqc.info/docs/ + licence: ["GPL-3.0-or-later"] + +input: + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. + pattern: "*.{yml,yaml}" + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + +output: + - report: + type: file + description: MultiQC report file + pattern: "multiqc_report.html" + - data: + type: directory + description: MultiQC data dir + pattern: "multiqc_data" + - plots: + type: file + description: Plots created by MultiQC + pattern: "*_data" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/nextflow.config b/nextflow.config index 0527f42..8f7d1d0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -13,6 +13,13 @@ params { // Input options input = null +// MultiQC options + multiqc_config = null + multiqc_title = null + multiqc_logo = null + max_multiqc_email_size = '25.MB' + multiqc_methods_description = null + // Boilerplate options outdir = null tracedir = "${params.outdir}/pipeline_info" @@ -26,7 +33,7 @@ params { version = false validate_params = true show_hidden_params = false - schema_ignore_params = 'fasta' + schema_ignore_params = 'genomes' // Config options @@ -66,7 +73,11 @@ try { profiles { - debug { process.beforeScript = 'echo $HOSTNAME' } + debug { + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + cleanup = false + } conda { conda.enabled = true docker.enabled = false @@ -74,6 +85,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } mamba { conda.enabled = true @@ -83,14 +95,18 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } docker { docker.enabled = true + docker.registry = 'quay.io' docker.userEmulation = true + conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' @@ -98,31 +114,49 @@ profiles { singularity { singularity.enabled = true singularity.autoMounts = true + conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } podman { podman.enabled = true + podman.registry = 'quay.io' + conda.enabled = false docker.enabled = false singularity.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } shifter { shifter.enabled = true + conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false charliecloud.enabled = false + apptainer.enabled = false } charliecloud { charliecloud.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + apptainer.enabled = false + } + apptainer { + apptainer.enabled = true + conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false + charliecloud.enabled = false } gitpod { executor.name = 'local' @@ -169,12 +203,12 @@ dag { manifest { name = 'sanger-tol/variantcalling' - author = """Guoying Qi""" + author = """@muffato, @gq1, @priyanka-surana""" homePage = 'https://github.com/sanger-tol/variantcalling' - description = """variant calling""" + description = """Variant calling pipeline for PacBio data using DeepVariant""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.0dev' + version = '1.0.0' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 73c70ad..cc5a4a1 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,8 +1,8 @@ { "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/sanger-tol/variantcalling/main/nextflow_schema.json", + "$id": "https://raw.githubusercontent.com/sanger-tol/variantcalling/master/nextflow_schema.json", "title": "sanger-tol/variantcalling pipeline parameters", - "description": "variant calling", + "description": "Variant calling pipeline for PacBio data using DeepVariant", "type": "object", "definitions": { "input_output_options": { @@ -34,6 +34,11 @@ "fa_icon": "fas fa-envelope", "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" + }, + "multiqc_title": { + "type": "string", + "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", + "fa_icon": "fas fa-file-signature" } } }, @@ -169,6 +174,14 @@ "fa_icon": "fas fa-remove-format", "hidden": true }, + "max_multiqc_email_size": { + "type": "string", + "description": "File size limit when attaching MultiQC reports to summary emails.", + "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", + "default": "25.MB", + "fa_icon": "fas fa-file-upload", + "hidden": true + }, "monochrome_logs": { "type": "boolean", "description": "Do not use coloured log outputs.", @@ -182,6 +195,23 @@ "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", "hidden": true }, + "multiqc_config": { + "type": "string", + "description": "Custom config file to supply to MultiQC.", + "fa_icon": "fas fa-cog", + "hidden": true + }, + "multiqc_logo": { + "type": "string", + "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file", + "fa_icon": "fas fa-image", + "hidden": true + }, + "multiqc_methods_description": { + "type": "string", + "description": "Custom MultiQC yaml file containing HTML including a methods description.", + "fa_icon": "fas fa-cog" + }, "tracedir": { "type": "string", "description": "Directory to keep pipeline Nextflow logs and reports.", diff --git a/pipeline_template.yml b/pipeline_template.yml index 0aa7398..09d0664 100644 --- a/pipeline_template.yml +++ b/pipeline_template.yml @@ -1,3 +1,3 @@ prefix: sanger-tol skip: - - igenomes +- igenomes diff --git a/tower.yml b/tower.yml new file mode 100644 index 0000000..787aedf --- /dev/null +++ b/tower.yml @@ -0,0 +1,5 @@ +reports: + multiqc_report.html: + display: "MultiQC HTML report" + samplesheet.csv: + display: "Auto-created samplesheet with collated metadata and FASTQ paths" diff --git a/workflows/variantcalling.nf b/workflows/variantcalling.nf index da91d34..59c0a7a 100644 --- a/workflows/variantcalling.nf +++ b/workflows/variantcalling.nf @@ -11,7 +11,7 @@ WorkflowVariantcalling.initialise(params, log) // TODO nf-core: Add all file path parameters for the pipeline to the list below // Check input path parameters to see if they exist -def checkPathParamList = [ params.input, params.fasta ] +def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ] for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } // Check mandatory parameters @@ -23,6 +23,11 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) +ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() +ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() +ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT LOCAL MODULES/SUBWORKFLOWS @@ -43,6 +48,8 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check' // // MODULE: Installed directly from nf-core/modules // +include { FASTQC } from '../modules/nf-core/fastqc/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' /* @@ -52,6 +59,7 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft */ // Info required for completion email and summary +def multiqc_report = [] workflow VARIANTCALLING { @@ -65,10 +73,40 @@ workflow VARIANTCALLING { ) ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) + // + // MODULE: Run FastQC + // + FASTQC ( + INPUT_CHECK.out.reads + ) + ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + CUSTOM_DUMPSOFTWAREVERSIONS ( ch_versions.unique().collectFile(name: 'collated_versions.yml') ) + // + // MODULE: MultiQC + // + workflow_summary = WorkflowVariantcalling.paramsSummaryMultiqc(workflow, summary_params) + ch_workflow_summary = Channel.value(workflow_summary) + + methods_description = WorkflowVariantcalling.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + ch_methods_description = Channel.value(methods_description) + + ch_multiqc_files = Channel.empty() + ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + + MULTIQC ( + ch_multiqc_files.collect(), + ch_multiqc_config.toList(), + ch_multiqc_custom_config.toList(), + ch_multiqc_logo.toList() + ) + multiqc_report = MULTIQC.out.report.toList() } /* @@ -79,7 +117,7 @@ workflow VARIANTCALLING { workflow.onComplete { if (params.email || params.email_on_fail) { - NfcoreTemplate.email(workflow, params, summary_params, projectDir, log) + NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) } NfcoreTemplate.summary(workflow, params, log) if (params.hook_url) { From e54a47afa9b483894e65383b0f9208b65b393fe7 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Thu, 21 Sep 2023 17:33:41 +0100 Subject: [PATCH 08/21] update the version to 1.1.0-dev --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 2363efa..8dba08f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -209,7 +209,7 @@ manifest { description = """Variant calling pipeline for PacBio data using DeepVariant""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.0.0' + version = '1.1.0-dev' doi = 'https://doi.org/10.5281/zenodo.7890527' } From 7d65f86aa940816f998b500e8fbc8abf1cf417eb Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Thu, 21 Sep 2023 17:37:04 +0100 Subject: [PATCH 09/21] missing bracks --- lib/WorkflowVariantcalling.groovy | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/WorkflowVariantcalling.groovy b/lib/WorkflowVariantcalling.groovy index 1b0fe03..d05a861 100755 --- a/lib/WorkflowVariantcalling.groovy +++ b/lib/WorkflowVariantcalling.groovy @@ -17,3 +17,4 @@ class WorkflowVariantcalling { Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." } } +} From 20062b4315a27dbb8a0dd763f9a342c547564817 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Thu, 21 Sep 2023 17:41:53 +0100 Subject: [PATCH 10/21] update the workflow because deepvaritant module updated. --- subworkflows/local/deepvariant_caller.nf | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/deepvariant_caller.nf b/subworkflows/local/deepvariant_caller.nf index 08adb0f..10b5359 100644 --- a/subworkflows/local/deepvariant_caller.nf +++ b/subworkflows/local/deepvariant_caller.nf @@ -22,13 +22,21 @@ workflow DEEPVARIANT_CALLER { .set { cram_crai } // fasta - fasta = reads_fasta.map { meta, cram, crai, interval, fasta_file_name, fasta, fai -> [ fasta ] } + fasta = reads_fasta.map { meta, cram, crai, interval, fasta_file_name, fasta, fai -> + [ [ id: meta.id + "_" + fasta_file_name, sample: meta.id, type: meta.type ], + fasta + ] + } // fai - fai = reads_fasta.map{ meta, cram, crai, interval, fasta_file_name, fasta, fai -> [ fai ] } + fai = reads_fasta.map{ meta, cram, crai, interval, fasta_file_name, fasta, fai -> + [ [ id: meta.id + "_" + fasta_file_name, sample: meta.id, type: meta.type ], + fai + ] + } // split fasta in compressed format, no gzi index file needed - gzi = [] + gzi = [ [], [] ] // call deepvariant DEEPVARIANT ( cram_crai, fasta, fai, gzi ) From 9a8be9030d48d87f8509d5a2784bd7f678b67d98 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Thu, 21 Sep 2023 17:44:46 +0100 Subject: [PATCH 11/21] nf-core modules update samtools/view --- modules.json | 2 +- modules/nf-core/samtools/view/main.nf | 4 ++-- modules/nf-core/samtools/view/meta.yml | 13 +++++++++---- 3 files changed, 12 insertions(+), 7 deletions(-) diff --git a/modules.json b/modules.json index 297798d..5d394c6 100644 --- a/modules.json +++ b/modules.json @@ -32,7 +32,7 @@ }, "samtools/view": { "branch": "master", - "git_sha": "371eff7748d769c2ddc8bd593773523a364a52fe", + "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f", "installed_by": ["modules"] } } diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index d7b2a0d..cb91fac 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -5,11 +5,11 @@ process SAMTOOLS_VIEW { conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'quay.io/biocontainers/samtools:1.17--h00cdaf9_0' }" + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(input), path(index) - path fasta + tuple val(meta2), path(fasta) path qname output: diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 7691603..3b05450 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -26,12 +26,17 @@ input: description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" - index: - type: optional file - description: BAM.BAI/BAM.CSI/CRAM.CRAI file + type: file + description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional) pattern: "*.{.bai,.csi,.crai}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - fasta: - type: optional file - description: Reference file the CRAM was created with + type: file + description: Reference file the CRAM was created with (optional) pattern: "*.{fasta,fa}" - qname: type: file From a4f703370c9ec6b2553394c4b4b67feb65026676 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Thu, 21 Sep 2023 17:57:54 +0100 Subject: [PATCH 12/21] update samtools view workflow because module updated --- subworkflows/local/input_filter_split.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/input_filter_split.nf b/subworkflows/local/input_filter_split.nf index f2f26c5..5963d36 100644 --- a/subworkflows/local/input_filter_split.nf +++ b/subworkflows/local/input_filter_split.nf @@ -62,7 +62,7 @@ workflow INPUT_FILTER_SPLIT { .set { fasta_fai } // filter reads - SAMTOOLS_VIEW ( reads, fasta, [] ) + SAMTOOLS_VIEW ( reads, [ [], fasta ], [] ) ch_versions = ch_versions.mix ( SAMTOOLS_VIEW.out.versions.first() ) // combine reads with splitted references From 048d08f867df6e4d05dfe5614fe1846f73ae9c7b Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Thu, 21 Sep 2023 17:59:18 +0100 Subject: [PATCH 13/21] nf-core modules update samtools/faidx --- modules.json | 2 +- modules/nf-core/samtools/faidx/main.nf | 18 ++++++++++++------ modules/nf-core/samtools/faidx/meta.yml | 14 ++++++++++++-- 3 files changed, 25 insertions(+), 9 deletions(-) diff --git a/modules.json b/modules.json index 5d394c6..bc363d0 100644 --- a/modules.json +++ b/modules.json @@ -27,7 +27,7 @@ }, "samtools/faidx": { "branch": "master", - "git_sha": "371eff7748d769c2ddc8bd593773523a364a52fe", + "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe", "installed_by": ["modules"] }, "samtools/view": { diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 21be8ba..59ed308 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -5,15 +5,17 @@ process SAMTOOLS_FAIDX { conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'quay.io/biocontainers/samtools:1.17--h00cdaf9_0' }" + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(fasta) + tuple val(meta2), path(fai) output: - tuple val(meta), path ("*.fai"), emit: fai - tuple val(meta), path ("*.gzi"), emit: gzi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path ("*.{fa,fasta}") , emit: fa , optional: true + tuple val(meta), path ("*.fai") , emit: fai, optional: true + tuple val(meta), path ("*.gzi") , emit: gzi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -23,8 +25,8 @@ process SAMTOOLS_FAIDX { """ samtools \\ faidx \\ - $args \\ - $fasta + $fasta \\ + $args cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -33,8 +35,12 @@ process SAMTOOLS_FAIDX { """ stub: + def match = (task.ext.args =~ /-o(?:utput)?\s(.*)\s?/).findAll() + def fastacmd = match[0] ? "touch ${match[0][1]}" : '' """ + ${fastacmd} touch ${fasta}.fai + cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index fe2fe9a..957b25e 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -3,6 +3,7 @@ description: Index FASTA file keywords: - index - fasta + - faidx tools: - samtools: description: | @@ -17,12 +18,21 @@ input: - meta: type: map description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Groovy Map containing reference information + e.g. [ id:'test' ] - fasta: type: file description: FASTA file pattern: "*.{fa,fasta}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" output: - meta: type: map From 555bc3da001b61bed56a576146db59ad0d6ddafe Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Thu, 21 Sep 2023 18:19:41 +0100 Subject: [PATCH 14/21] update workflow because samtools faidx module updated --- subworkflows/local/input_filter_split.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/input_filter_split.nf b/subworkflows/local/input_filter_split.nf index 5963d36..c820901 100644 --- a/subworkflows/local/input_filter_split.nf +++ b/subworkflows/local/input_filter_split.nf @@ -49,7 +49,7 @@ workflow INPUT_FILTER_SPLIT { .set { split_fasta } // index split fasta files - SAMTOOLS_FAIDX ( split_fasta ) + SAMTOOLS_FAIDX ( split_fasta, [[], []]) ch_versions = ch_versions.mix( SAMTOOLS_FAIDX.out.versions.first() ) // join fasta with corresponding fai file From 6c4804be03d4b71348859b149ea1fedb10429f3b Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Thu, 21 Sep 2023 18:23:01 +0100 Subject: [PATCH 15/21] use version 2.8 for nf-core lint in github --- .github/workflows/linting.yml | 2 +- .nf-core.yml | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 888cb4b..c20e72b 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -84,7 +84,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core + pip install nf-core==2.8.0 - name: Run nf-core lint env: diff --git a/.nf-core.yml b/.nf-core.yml index f58cf3f..4e011f7 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -16,6 +16,7 @@ lint: - lib/NfcoreTemplate.groovy - .github/PULL_REQUEST_TEMPLATE.md - .github/workflows/branch.yml + - .github/workflows/linting.yml - LICENSE - assets/email_template.html - .github/ISSUE_TEMPLATE/bug_report.yml From 07716c2cb48c76c29fad7e9af23ee1ab546d1961 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Thu, 21 Sep 2023 18:30:46 +0100 Subject: [PATCH 16/21] remove white space --- lib/WorkflowVariantcalling.groovy | 1 - 1 file changed, 1 deletion(-) diff --git a/lib/WorkflowVariantcalling.groovy b/lib/WorkflowVariantcalling.groovy index d05a861..523a779 100755 --- a/lib/WorkflowVariantcalling.groovy +++ b/lib/WorkflowVariantcalling.groovy @@ -11,7 +11,6 @@ class WorkflowVariantcalling { // Check and validate parameters // public static void initialise(params, log) { - if (!params.fasta) { Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." From 9e731d7061d7aaa892436f6e4472127e49429381 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Thu, 21 Sep 2023 18:37:19 +0100 Subject: [PATCH 17/21] prettier --- .github/workflows/linting.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index c20e72b..3f27dab 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -84,7 +84,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core==2.8.0 + pip install nf-core==2.8.0 - name: Run nf-core lint env: From b302172850a721b98238f84d842c987389b24c2c Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Thu, 21 Sep 2023 18:53:40 +0100 Subject: [PATCH 18/21] to fail prettier --- .github/workflows/linting.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 3f27dab..c20e72b 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -84,7 +84,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core==2.8.0 + pip install nf-core==2.8.0 - name: Run nf-core lint env: From d50080ef2750b01fe5da3af9a031e286fcf571b4 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 21 Sep 2023 17:54:47 +0000 Subject: [PATCH 19/21] [automated] Fix linting with Prettier --- .github/workflows/linting.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index c20e72b..3f27dab 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -84,7 +84,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core==2.8.0 + pip install nf-core==2.8.0 - name: Run nf-core lint env: From f5a1186549dc155bad81622202462bdb15ebe2d1 Mon Sep 17 00:00:00 2001 From: Priyanka Surana Date: Tue, 26 Sep 2023 17:24:42 +0100 Subject: [PATCH 20/21] Update nextflow.config --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index 8dba08f..83e274f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -115,6 +115,7 @@ profiles { singularity { singularity.enabled = true singularity.autoMounts = true + singularity.registry = 'quay.io' conda.enabled = false docker.enabled = false podman.enabled = false From fe45c30046d4d0eaaf30a0ea156c881035919e9d Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Tue, 26 Sep 2023 17:27:11 +0100 Subject: [PATCH 21/21] update the display text. --- tower.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tower.yml b/tower.yml index c61323c..48611ab 100644 --- a/tower.yml +++ b/tower.yml @@ -1,3 +1,3 @@ reports: samplesheet.csv: - display: "Auto-created samplesheet with collated metadata and FASTQ paths" + display: "Auto-created samplesheet with collated metadata and aligned file paths."