From 5f4f3386c62bb6cb896465922d13a98ebcf6fbdb Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 12 May 2023 13:36:15 +0000 Subject: [PATCH 01/33] Bump to 2.3.0dev --- CHANGELOG.md | 5 ++++- nextflow.config | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8024dbeb..2a55827c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,10 @@ 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). -## [v2.2.1](https://github.com/nf-core/smrnaseq/releases/tag/2.2.1) - 2023-05-08 +## Current dev + +Nothing yet +## [v2.2.1](https://github.com/nf-core/smrnaseq/releases/tag/2.2.1) - 2023-05-12 ### Enhancements & fixes diff --git a/nextflow.config b/nextflow.config index 2f9dd945..68d6dee4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -259,7 +259,7 @@ manifest { description = """Small RNA-Seq Best Practice Analysis Pipeline.""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '2.2.1' + version = '2.3.0dev' doi = '' } From dd0595f38d4eea49c113ab3425d831f9727344dd Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Wed, 31 May 2023 11:36:09 +0100 Subject: [PATCH 02/33] Remove glob from process definition when using ECR container --- CHANGELOG.md | 3 ++- conf/public_aws_ecr.config | 10 +++++----- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2a55827c..ba115168 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## Current dev -Nothing yet +- Remove globs from process alias when using ECR containers + ## [v2.2.1](https://github.com/nf-core/smrnaseq/releases/tag/2.2.1) - 2023-05-12 ### Enhancements & fixes diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config index 8152e14a..39c8f881 100644 --- a/conf/public_aws_ecr.config +++ b/conf/public_aws_ecr.config @@ -12,19 +12,19 @@ docker.registry = 'public.ecr.aws' podman.registry = 'public.ecr.aws' process { - withName: '.*:SAMPLESHEET_CHECK' { + withName: 'SAMPLESHEET_CHECK' { container = "quay.io/biocontainers/python:3.8.3" } - withName: '.*:BOWTIE_MAP.*' { + withName: 'BOWTIE_MAP' { container = 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0' } - withName: '.*:EDGER_QC' { + withName: 'EDGER_QC' { container = 'quay.io/biocontainers/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:709335c37934db1b481054cbec637c6e5b5971cb-0' } - withName: '.*:MIRTOP_QUANT' { + withName: 'MIRTOP_QUANT' { container = 'quay.io/biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' } - withName: '.*:TABLE_MERGE' { + withName: 'TABLE_MERGE' { container = 'quay.io/biocontainers/r-data.table:1.12.2' } } From dbe981d2006f679484b8ec3a0c5bd0799d06bb00 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Wed, 31 May 2023 11:38:59 +0100 Subject: [PATCH 03/33] fixup --- conf/public_aws_ecr.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config index 39c8f881..4febe35f 100644 --- a/conf/public_aws_ecr.config +++ b/conf/public_aws_ecr.config @@ -15,7 +15,7 @@ process { withName: 'SAMPLESHEET_CHECK' { container = "quay.io/biocontainers/python:3.8.3" } - withName: 'BOWTIE_MAP' { + withName: 'BOWTIE_MAP.*' { container = 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0' } withName: 'EDGER_QC' { From 0e76821dd3ae4aac9f265b029bfcd8c00a8f2ef4 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Wed, 31 May 2023 11:40:23 +0100 Subject: [PATCH 04/33] Changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ba115168..1dcf9a6a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## Current dev -- Remove globs from process alias when using ECR containers +- [[#253]](https://github.com/nf-core/smrnaseq/pull/253) - Remove globs from process alias when using ECR containers ## [v2.2.1](https://github.com/nf-core/smrnaseq/releases/tag/2.2.1) - 2023-05-12 From f570c385c1364831045fe72332b026f01c40edfd Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 31 May 2023 16:47:55 +0200 Subject: [PATCH 05/33] Apply suggestions from code review --- CHANGELOG.md | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1dcf9a6a..5553c523 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). -## Current dev +## [v2.2.2](https://github.com/nf-core/smrnaseq/releases/tag/2.2.2) - 2023-06-01``` - [[#253]](https://github.com/nf-core/smrnaseq/pull/253) - Remove globs from process alias when using ECR containers diff --git a/nextflow.config b/nextflow.config index 68d6dee4..5a6952df 100644 --- a/nextflow.config +++ b/nextflow.config @@ -259,7 +259,7 @@ manifest { description = """Small RNA-Seq Best Practice Analysis Pipeline.""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '2.3.0dev' + version = '2.2.2' doi = '' } From 16ac6b2611ae686cd4db70356eaa421b281eb438 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 31 May 2023 16:48:16 +0200 Subject: [PATCH 06/33] Apply suggestions from code review --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5553c523..c5b5af39 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). -## [v2.2.2](https://github.com/nf-core/smrnaseq/releases/tag/2.2.2) - 2023-06-01``` +## [v2.2.2](https://github.com/nf-core/smrnaseq/releases/tag/2.2.2) - 2023-06-01 - [[#253]](https://github.com/nf-core/smrnaseq/pull/253) - Remove globs from process alias when using ECR containers From dd3e01677061777d3aa4d92839b3814d25330d10 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 31 May 2023 16:51:03 +0200 Subject: [PATCH 07/33] Update ci.yml --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c4bd5555..1afd21e8 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.1" - "latest-everything" profile: - "test" From dda769d91c14b79e3a1d922bf2f6bd3ae8cab90b Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 19 Jun 2023 13:51:11 +0000 Subject: [PATCH 08/33] Remove public_aws_ecr profile --- .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awstest.yml | 2 +- CHANGELOG.md | 4 ++++ conf/public_aws_ecr.config | 30 ------------------------------ nextflow.config | 3 --- 5 files changed, 6 insertions(+), 35 deletions(-) delete mode 100644 conf/public_aws_ecr.config diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index f96fb17c..5d00bc97 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -24,7 +24,7 @@ jobs: { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/smrnaseq/results-${{ github.sha }}" } - profiles: test_full,public_aws_ecr + profiles: test_full - uses: actions/upload-artifact@v3 with: name: Tower debug log file diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index a1f96d73..7d4c357c 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -22,7 +22,7 @@ jobs: { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/smrnaseq/results-test-${{ github.sha }}" } - profiles: test,public_aws_ecr + profiles: test - uses: actions/upload-artifact@v3 with: name: Tower debug log file diff --git a/CHANGELOG.md b/CHANGELOG.md index c5b5af39..2ca1a1cc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## dev + +- Remove public_aws_ecr profile + ## [v2.2.2](https://github.com/nf-core/smrnaseq/releases/tag/2.2.2) - 2023-06-01 - [[#253]](https://github.com/nf-core/smrnaseq/pull/253) - Remove globs from process alias when using ECR containers diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config deleted file mode 100644 index 4febe35f..00000000 --- a/conf/public_aws_ecr.config +++ /dev/null @@ -1,30 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - AWS ECR Config -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Config to set public AWS ECR images wherever possible - This improves speed when running on AWS infrastructure. - Use this as an example template when using your own private registry. ----------------------------------------------------------------------------------------- -*/ - -docker.registry = 'public.ecr.aws' -podman.registry = 'public.ecr.aws' - -process { - withName: 'SAMPLESHEET_CHECK' { - container = "quay.io/biocontainers/python:3.8.3" - } - withName: 'BOWTIE_MAP.*' { - container = 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0' - } - withName: 'EDGER_QC' { - container = 'quay.io/biocontainers/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:709335c37934db1b481054cbec637c6e5b5971cb-0' - } - withName: 'MIRTOP_QUANT' { - container = 'quay.io/biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' - } - withName: 'TABLE_MERGE' { - container = 'quay.io/biocontainers/r-data.table:1.12.2' - } -} diff --git a/nextflow.config b/nextflow.config index 5a6952df..ecaa7ccb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -199,9 +199,6 @@ profiles { executor.cpus = 16 executor.memory = 60.GB } - public_aws_ecr { - includeConfig 'conf/public_aws_ecr.config' - } test { includeConfig 'conf/test.config' } test_no_genome { includeConfig 'conf/test_no_genome.config' } test_full { includeConfig 'conf/test_full.config' } From 891ccfaa00bb9496d2f99d8551a5371ed8e6d759 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Tue, 27 Jun 2023 09:21:35 +0100 Subject: [PATCH 09/33] Min nextflow test 22.10.1 --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1afd21e8..c4bd5555 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "23.04.1" + - "22.10.1" - "latest-everything" profile: - "test" From 7ea85c446f542dae37fb7b960dd37d18b0afb6d3 Mon Sep 17 00:00:00 2001 From: Rob Syme Date: Wed, 23 Aug 2023 12:58:33 -0400 Subject: [PATCH 10/33] Mirbase has changed their URL structure, so we need to update the URLs in the configuration files and docs. Signed-off-by: Rob Syme --- docs/usage.md | 6 +++--- nextflow.config | 4 ++-- nextflow_schema.json | 6 +++--- workflows/smrnaseq.nf | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 1893e2e6..7a01c1fa 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -26,9 +26,9 @@ It should point to the 3-letter species name used by [miRBase](https://www.mirba Different parameters can be set for the two supported databases. By default `miRBase` will be used with the parameters below. -- `mirna_gtf`: If not supplied by the user, then `mirna_gtf` will point to the latest GFF3 file in miRbase: `https://mirbase.org/ftp/CURRENT/genomes/${params.mirtrace_species}.gff3` -- `mature`: points to the FASTA file of mature miRNA sequences. `https://mirbase.org/ftp/CURRENT/mature.fa.gz` -- `hairpin`: points to the FASTA file of precursor miRNA sequences. `https://mirbase.org/ftp/CURRENT/hairpin.fa.gz` +- `mirna_gtf`: If not supplied by the user, then `mirna_gtf` will point to the latest GFF3 file in miRbase: `https://mirbase.org/download/CURRENT/genomes/${params.mirtrace_species}.gff3` +- `mature`: points to the FASTA file of mature miRNA sequences. `https://mirbase.org/download/CURRENT/mature.fa` +- `hairpin`: points to the FASTA file of precursor miRNA sequences. `https://mirbase.org/download/CURRENT/hairpin.fa` If MirGeneDB should be used instead it needs to be specified using `--mirgenedb` and use the parameters below . diff --git a/nextflow.config b/nextflow.config index ecaa7ccb..61114b48 100644 --- a/nextflow.config +++ b/nextflow.config @@ -20,8 +20,8 @@ params { igenomes_base = 's3://ngi-igenomes/igenomes' igenomes_ignore = false mirna_gtf = null - mature = "https://mirbase.org/ftp/CURRENT/mature.fa.gz" - hairpin = "https://mirbase.org/ftp/CURRENT/hairpin.fa.gz" + mature = "https://mirbase.org/download/CURRENT/mature.fa" + hairpin = "https://mirbase.org/download/CURRENT/hairpin.fa" mirgenedb = false mirgenedb_mature = null mirgenedb_hairpin = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 213199c1..48fda3e7 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -87,7 +87,7 @@ "mirna_gtf": { "type": "string", "description": "GFF/GTF file with coordinates positions of precursor and miRNAs.", - "help_text": "miRBase `.gff3` file, typically downloaded from [`https://mirbase.org/ftp/CURRENT/genomes/`](https://mirbase.org/ftp/CURRENT/genomes/)\n\nIf using iGenomes with `--genome` this file will be downloaded from miRBase automatically during the pipeline run.\n\n", + "help_text": "miRBase `.gff3` file, typically downloaded from [`https://mirbase.org/download/CURRENT/genomes/`](https://mirbase.org/download/CURRENT/genomes/)\n\nIf using iGenomes with `--genome` this file will be downloaded from miRBase automatically during the pipeline run.\n\n", "fa_icon": "fas fa-address-book" }, "mirgenedb_gff": { @@ -100,7 +100,7 @@ "description": "Path to FASTA file with mature miRNAs.", "fa_icon": "fas fa-wheelchair", "help_text": "Typically this will be the `mature.fa` file from miRBase. Can be given either as a plain text `.fa` file or a compressed `.gz` file.\n\nDefaults to the current miRBase release URL, from which the file will be downloaded.", - "default": "https://mirbase.org/ftp/CURRENT/mature.fa.gz" + "default": "https://mirbase.org/download/CURRENT/mature.fa" }, "mirgenedb_mature": { "type": "string", @@ -112,7 +112,7 @@ "description": "Path to FASTA file with miRNAs precursors.", "fa_icon": "fab fa-cuttlefish", "help_text": "Typically this will be the `mature.fa` file from miRBase. Can be given either as a plain text `.fa` file or a compressed `.gz` file.\n\nDefaults to the current miRBase release URL, from which the file will be downloaded.", - "default": "https://mirbase.org/ftp/CURRENT/hairpin.fa.gz" + "default": "https://mirbase.org/download/CURRENT/hairpin.fa" }, "mirgenedb_hairpin": { "type": "string", diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf index ad5ecfef..ed8f87c8 100644 --- a/workflows/smrnaseq.nf +++ b/workflows/smrnaseq.nf @@ -25,7 +25,7 @@ if (!params.mirtrace_species) { } // Genome options -def mirna_gtf_from_species = params.mirtrace_species ? "https://mirbase.org/ftp/CURRENT/genomes/${params.mirtrace_species}.gff3" : false +def mirna_gtf_from_species = params.mirtrace_species ? "https://mirbase.org/download/CURRENT/genomes/${params.mirtrace_species}.gff3" : false def mirna_gtf = params.mirna_gtf ?: mirna_gtf_from_species /* From d3a0df94251016cdb006dcb3521969b2119dcb4e Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 30 Aug 2023 06:57:12 +0000 Subject: [PATCH 11/33] Template merge and modules updates --- .github/CONTRIBUTING.md | 1 - .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/workflows/awsfulltest.yml | 9 +- .github/workflows/awstest.yml | 8 +- .github/workflows/ci.yml | 2 +- .gitpod.yml | 5 + CITATIONS.md | 5 + README.md | 6 +- assets/methods_description_template.yml | 10 +- assets/multiqc_config.yml | 4 +- assets/nf-core-smrnaseq_logo_light.png | Bin 11484 -> 74188 bytes assets/slackreport.json | 2 +- docs/usage.md | 6 +- lib/NfcoreSchema.groovy | 530 ------------------------ lib/NfcoreTemplate.groovy | 2 +- lib/WorkflowMain.groovy | 32 -- lib/WorkflowSmrnaseq.groovy | 45 +- main.nf | 16 + nextflow.config | 42 +- nextflow_schema.json | 37 +- workflows/smrnaseq.nf | 17 +- 21 files changed, 174 insertions(+), 607 deletions(-) delete mode 100755 lib/NfcoreSchema.groovy diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index b24dd094..33a2c027 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -116,4 +116,3 @@ To get started: Devcontainer specs: - [DevContainer config](.devcontainer/devcontainer.json) -- [Dockerfile](.devcontainer/Dockerfile) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 137da49f..335a06b1 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -42,7 +42,7 @@ body: attributes: label: System information description: | - * Nextflow version _(eg. 22.10.1)_ + * Nextflow version _(eg. 23.04.0)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 5d00bc97..2ac5826b 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,18 +14,23 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/smrnaseq/work-${{ github.sha }} parameters: | { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/smrnaseq/results-${{ github.sha }}" } profiles: test_full + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 7d4c357c..84d22f1c 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,18 +12,22 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/smrnaseq/work-${{ github.sha }} parameters: | { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/smrnaseq/results-test-${{ github.sha }}" } profiles: test + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c4bd5555..45ad5219 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" profile: - "test" diff --git a/.gitpod.yml b/.gitpod.yml index 85d95ecc..25488dcc 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,9 @@ image: nfcore/gitpod:latest +tasks: + - name: Update Nextflow and setup pre-commit + command: | + pre-commit install --install-hooks + nextflow self-update vscode: extensions: # based on nf-core.nf-core-extensionpack diff --git a/CITATIONS.md b/CITATIONS.md index 11f752b9..67b98c96 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,6 +12,8 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + * [trimgalore](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) * [samtools](https://pubmed.ncbi.nlm.nih.gov/19505943/) @@ -56,5 +58,8 @@ - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. + - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) + > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. diff --git a/README.md b/README.md index 6fb16c5e..24226773 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/smrnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3456879-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3456879) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -92,11 +92,11 @@ nextflow run nf-core/smrnaseq \ > 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). -For more details, please refer to the [usage documentation](https://nf-co.re/smrnaseq/usage) and the [parameter documentation](https://nf-co.re/smrnaseq/parameters). +For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/smrnaseq/usage) and the [parameter documentation](https://nf-co.re/smrnaseq/parameters). ## Pipeline output -To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/smrnaseq/results) tab on the nf-core website pipeline page. +To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/smrnaseq/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/smrnaseq/output). diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 1f05424e..87cc6194 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -5,13 +5,17 @@ section_href: "https://github.com/nf-core/smrnaseq" plot_type: "html" data: |

Methods

-

Data was processed using nf-core/smrnaseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

+

Data was processed using nf-core/smrnaseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}
+

${tool_citations}

References

    -
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
  • -
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
  • +
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
  • +
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
  • +
  • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
  • +
  • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
  • + ${tool_bibliography}
Notes:
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index df5ec37a..23da1135 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/smrnaseq + This report has been generated by the nf-core/smrnaseq analysis pipeline. 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{ %>danger<%} %>", - "author_name": "sanger-tol/readmapping v${version} - ${runName}", + "author_name": "nf-core/smrnaseq v${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/docs/usage.md b/docs/usage.md index 1893e2e6..f7810e59 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -104,7 +104,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/smrnaseq --input samplesheet.csv --outdir --genome GRCh37 -profile docker +nextflow run nf-core/smrnaseq --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -123,7 +123,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than 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: + +The above pipeline run specified with a params file in yaml format: ```bash nextflow run nf-core/smrnaseq -profile docker -params-file params.yaml @@ -135,7 +136,6 @@ with `params.yaml` containing: input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' -input: 'data' <...> ``` diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy deleted file mode 100755 index 9b34804d..00000000 --- a/lib/NfcoreSchema.groovy +++ /dev/null @@ -1,530 +0,0 @@ -// -// 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 -import org.json.JSONObject -import org.json.JSONTokener -import org.json.JSONArray -import groovy.json.JsonSlurper -import groovy.json.JsonBuilder - -class NfcoreSchema { - - // - // Resolve Schema path relative to main workflow directory - // - public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') { - return "${workflow.projectDir}/${schema_filename}" - } - - // - // Function to loop over all parameters defined in schema and check - // whether the given parameters adhere to the specifications - // - /* groovylint-disable-next-line UnusedPrivateMethodParameter */ - public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') { - def has_error = false - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Check for nextflow core params and unexpected params - def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text - def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions') - def nf_params = [ - // Options for base `nextflow` command - 'bg', - 'c', - 'C', - 'config', - 'd', - 'D', - 'dockerize', - 'h', - 'log', - 'q', - 'quiet', - 'syslog', - 'v', - - // Options for `nextflow run` command - 'ansi', - 'ansi-log', - 'bg', - 'bucket-dir', - 'c', - 'cache', - 'config', - 'dsl2', - 'dump-channels', - 'dump-hashes', - 'E', - 'entry', - 'latest', - 'lib', - 'main-script', - 'N', - 'name', - 'offline', - 'params-file', - 'pi', - 'plugins', - 'poll-interval', - 'pool-size', - 'profile', - 'ps', - 'qs', - 'queue-size', - 'r', - 'resume', - 'revision', - 'stdin', - 'stub', - 'stub-run', - 'test', - 'w', - 'with-apptainer', - 'with-charliecloud', - 'with-conda', - 'with-dag', - 'with-docker', - 'with-mpi', - 'with-notification', - 'with-podman', - 'with-report', - 'with-singularity', - 'with-timeline', - 'with-tower', - 'with-trace', - 'with-weblog', - 'without-docker', - 'without-podman', - 'work-dir' - ] - def unexpectedParams = [] - - // Collect expected parameters from the schema - def expectedParams = [] - def enums = [:] - for (group in schemaParams) { - for (p in group.value['properties']) { - expectedParams.push(p.key) - if (group.value['properties'][p.key].containsKey('enum')) { - enums[p.key] = group.value['properties'][p.key]['enum'] - } - } - } - - for (specifiedParam in params.keySet()) { - // nextflow params - if (nf_params.contains(specifiedParam)) { - log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'" - has_error = true - } - // unexpected params - def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params' - def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() } - def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase() - def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase)) - if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) { - // Temporarily remove camelCase/camel-case params #1035 - def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()} - if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){ - unexpectedParams.push(specifiedParam) - } - } - } - - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Validate parameters against the schema - InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream() - JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream)) - - // Remove anything that's in params.schema_ignore_params - raw_schema = removeIgnoredParams(raw_schema, params) - - Schema schema = SchemaLoader.load(raw_schema) - - // Clean the parameters - def cleanedParams = cleanParameters(params) - - // Convert to JSONObject - def jsonParams = new JsonBuilder(cleanedParams) - JSONObject params_json = new JSONObject(jsonParams.toString()) - - // Validate - try { - schema.validate(params_json) - } catch (ValidationException e) { - println '' - log.error 'ERROR: Validation of pipeline parameters failed!' - JSONObject exceptionJSON = e.toJSON() - printExceptions(exceptionJSON, params_json, log, enums) - println '' - has_error = true - } - - // Check for unexpected parameters - if (unexpectedParams.size() > 0) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - println '' - def warn_msg = 'Found unexpected parameters:' - for (unexpectedParam in unexpectedParams) { - warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}" - } - log.warn warn_msg - log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}" - println '' - } - - if (has_error) { - Nextflow.error('Exiting!') - } - } - - // - // Beautify parameters for --help - // - public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - Integer num_hidden = 0 - String output = '' - output += 'Typical pipeline command:\n\n' - output += " ${colors.cyan}${command}${colors.reset}\n\n" - Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - Integer max_chars = paramsMaxChars(params_map) + 1 - Integer desc_indent = max_chars + 14 - Integer dec_linewidth = 160 - desc_indent - for (group in params_map.keySet()) { - Integer num_params = 0 - String group_output = colors.underlined + colors.bold + group + colors.reset + '\n' - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (group_params.get(param).hidden && !params.show_hidden_params) { - num_hidden += 1 - continue; - } - def type = '[' + group_params.get(param).type + ']' - def description = group_params.get(param).description - def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : '' - def description_default = description + colors.dim + defaultValue + colors.reset - // Wrap long description texts - // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap - if (description_default.length() > dec_linewidth){ - List olines = [] - String oline = "" // " " * indent - description_default.split(" ").each() { wrd -> - if ((oline.size() + wrd.size()) <= dec_linewidth) { - oline += wrd + " " - } else { - olines += oline - oline = wrd + " " - } - } - olines += oline - description_default = olines.join("\n" + " " * desc_indent) - } - group_output += " --" + param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n' - num_params += 1 - } - group_output += '\n' - if (num_params > 0){ - output += group_output - } - } - if (num_hidden > 0){ - output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset - } - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Groovy Map summarising parameters/workflow options used by the pipeline - // - public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') { - // Get a selection of core Nextflow workflow options - def Map workflow_summary = [:] - if (workflow.revision) { - workflow_summary['revision'] = workflow.revision - } - workflow_summary['runName'] = workflow.runName - if (workflow.containerEngine) { - workflow_summary['containerEngine'] = workflow.containerEngine - } - if (workflow.container) { - workflow_summary['container'] = workflow.container - } - workflow_summary['launchDir'] = workflow.launchDir - workflow_summary['workDir'] = workflow.workDir - workflow_summary['projectDir'] = workflow.projectDir - workflow_summary['userName'] = workflow.userName - workflow_summary['profile'] = workflow.profile - workflow_summary['configFiles'] = workflow.configFiles.join(', ') - - // Get pipeline parameters defined in JSON Schema - def Map params_summary = [:] - def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - for (group in params_map.keySet()) { - def sub_params = new LinkedHashMap() - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (params.containsKey(param)) { - def params_value = params.get(param) - def schema_value = group_params.get(param).default - def param_type = group_params.get(param).type - if (schema_value != null) { - if (param_type == 'string') { - if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) { - def sub_string = schema_value.replace('\$projectDir', '') - sub_string = sub_string.replace('\${projectDir}', '') - if (params_value.contains(sub_string)) { - schema_value = params_value - } - } - if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) { - def sub_string = schema_value.replace('\$params.outdir', '') - sub_string = sub_string.replace('\${params.outdir}', '') - if ("${params.outdir}${sub_string}" == params_value) { - schema_value = params_value - } - } - } - } - - // We have a default in the schema, and this isn't it - if (schema_value != null && params_value != schema_value) { - sub_params.put(param, params_value) - } - // No default in the schema, and this isn't empty - else if (schema_value == null && params_value != "" && params_value != null && params_value != false) { - sub_params.put(param, params_value) - } - } - } - params_summary.put(group, sub_params) - } - return [ 'Core Nextflow options' : workflow_summary ] << params_summary - } - - // - // Beautify parameters for summary and return as string - // - public static String paramsSummaryLog(workflow, params) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - String output = '' - def params_map = paramsSummaryMap(workflow, params) - def max_chars = paramsMaxChars(params_map) - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - if (group_params) { - output += colors.bold + group + colors.reset + '\n' - for (param in group_params.keySet()) { - output += " " + colors.blue + param.padRight(max_chars) + ": " + colors.green + group_params.get(param) + colors.reset + '\n' - } - output += '\n' - } - } - output += "!! Only displaying parameters that differ from the pipeline defaults !!\n" - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Loop over nested exceptions and print the causingException - // - private static void printExceptions(ex_json, params_json, log, enums, limit=5) { - def causingExceptions = ex_json['causingExceptions'] - if (causingExceptions.length() == 0) { - def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/ - // Missing required param - if (m.matches()) { - log.error "* Missing required parameter: --${m[0][1]}" - } - // Other base-level error - else if (ex_json['pointerToViolation'] == '#') { - log.error "* ${ex_json['message']}" - } - // Error with specific param - else { - def param = ex_json['pointerToViolation'] - ~/^#\// - def param_val = params_json[param].toString() - if (enums.containsKey(param)) { - def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices" - if (enums[param].size() > limit) { - log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )" - } else { - log.error "${error_msg}: ${enums[param].join(', ')})" - } - } else { - log.error "* --${param}: ${ex_json['message']} (${param_val})" - } - } - } - for (ex in causingExceptions) { - printExceptions(ex, params_json, log, enums) - } - } - - // - // Remove an element from a JSONArray - // - private static JSONArray removeElement(json_array, element) { - def list = [] - int len = json_array.length() - for (int i=0;i - if(raw_schema.keySet().contains('definitions')){ - raw_schema.definitions.each { definition -> - for (key in definition.keySet()){ - if (definition[key].get("properties").keySet().contains(ignore_param)){ - // Remove the param to ignore - definition[key].get("properties").remove(ignore_param) - // If the param was required, change this - if (definition[key].has("required")) { - def cleaned_required = removeElement(definition[key].required, ignore_param) - definition[key].put("required", cleaned_required) - } - } - } - } - } - if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) { - raw_schema.get("properties").remove(ignore_param) - } - if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) { - def cleaned_required = removeElement(raw_schema.required, ignore_param) - raw_schema.put("required", cleaned_required) - } - } - return raw_schema - } - - // - // Clean and check parameters relative to Nextflow native classes - // - private static Map cleanParameters(params) { - def new_params = params.getClass().newInstance(params) - for (p in params) { - // remove anything evaluating to false - if (!p['value']) { - new_params.remove(p.key) - } - // Cast MemoryUnit to String - if (p['value'].getClass() == nextflow.util.MemoryUnit) { - new_params.replace(p.key, p['value'].toString()) - } - // Cast Duration to String - if (p['value'].getClass() == nextflow.util.Duration) { - new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day")) - } - // Cast LinkedHashMap to String - if (p['value'].getClass() == LinkedHashMap) { - new_params.replace(p.key, p['value'].toString()) - } - } - return new_params - } - - // - // This function tries to read a JSON params file - // - private static LinkedHashMap paramsLoad(String json_schema) { - def params_map = new LinkedHashMap() - try { - params_map = paramsRead(json_schema) - } catch (Exception e) { - println "Could not read parameters settings from JSON. $e" - params_map = new LinkedHashMap() - } - return params_map - } - - // - // Method to actually read in JSON file using Groovy. - // Group (as Key), values are all parameters - // - Parameter1 as Key, Description as Value - // - Parameter2 as Key, Description as Value - // .... - // Group - // - - private static LinkedHashMap paramsRead(String json_schema) throws Exception { - def json = new File(json_schema).text - def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions') - def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties') - /* Tree looks like this in nf-core schema - * definitions <- this is what the first get('definitions') gets us - group 1 - title - description - properties - parameter 1 - type - description - parameter 2 - type - description - group 2 - title - description - properties - parameter 1 - type - description - * properties <- parameters can also be ungrouped, outside of definitions - parameter 1 - type - description - */ - - // Grouped params - def params_map = new LinkedHashMap() - schema_definitions.each { key, val -> - def Map group = schema_definitions."$key".properties // Gets the property object of the group - def title = schema_definitions."$key".title - def sub_params = new LinkedHashMap() - group.each { innerkey, value -> - sub_params.put(innerkey, value) - } - params_map.put(title, sub_params) - } - - // Ungrouped params - def ungrouped_params = new LinkedHashMap() - schema_properties.each { innerkey, value -> - ungrouped_params.put(innerkey, value) - } - params_map.put("Other parameters", ungrouped_params) - - return params_map - } - - // - // Get maximum number of characters across all parameter names - // - private static Integer paramsMaxChars(params_map) { - Integer max_chars = 0 - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (param.size() > max_chars) { - max_chars = param.size() - } - } - } - return max_chars - } -} diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 25a0a74a..408951ae 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -128,7 +128,7 @@ class NfcoreTemplate { def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] def sf = new File("$projectDir/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 9a0db96c..ed5a126c 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -19,30 +19,6 @@ class WorkflowMain { " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } - // - // Generate help string - // - public static String help(workflow, params) { - def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" - def help_string = '' - help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) - help_string += NfcoreSchema.paramsHelp(workflow, params, command) - help_string += '\n' + citation(workflow) + '\n' - help_string += NfcoreTemplate.dashedLine(params.monochrome_logs) - return help_string - } - - // - // Generate parameter summary log string - // - public static String paramsSummaryLog(workflow, params) { - def summary_log = '' - summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) - summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) - summary_log += '\n' + citation(workflow) + '\n' - summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs) - return summary_log - } // // Validate parameters and print summary to screen @@ -65,14 +41,6 @@ class WorkflowMain { System.exit(0) } - // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params) - - // Validate workflow parameters via the JSON schema - if (params.validate_params) { - NfcoreSchema.validateParameters(workflow, params, log) - } - // Check that a -profile or Nextflow config has been provided to run the pipeline NfcoreTemplate.checkConfigProvided(workflow, log) diff --git a/lib/WorkflowSmrnaseq.groovy b/lib/WorkflowSmrnaseq.groovy index 7013e903..703c1342 100755 --- a/lib/WorkflowSmrnaseq.groovy +++ b/lib/WorkflowSmrnaseq.groovy @@ -11,6 +11,7 @@ class WorkflowSmrnaseq { // Check and validate parameters // public static void initialise(params, log) { + genomeExistsError(params, log) } @@ -41,15 +42,57 @@ class WorkflowSmrnaseq { return yaml_file_text } - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // + // Generate methods description for MultiQC + // + + public static String toolCitationText(params) { + + // TODO Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text + } + + public static String toolBibliographyText(params) { + + // TODO Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "

  • Author (2023) Pub name, Journal, DOI
  • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
  • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
  • " + ].join(' ').trim() + + return reference_text + } + + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { // 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() + // Pipeline DOI meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
  • " + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + //meta["tool_bibliography"] = toolBibliographyText(params) + + def methods_text = mqc_methods_yaml.text def engine = new SimpleTemplateEngine() diff --git a/main.nf b/main.nf index 68e88980..e0072925 100644 --- a/main.nf +++ b/main.nf @@ -27,6 +27,22 @@ params.bowtie_index = WorkflowMain.getGenomeAttribute(params, 'bowtie') ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { validateParameters; paramsHelp } from 'plugin/nf-validation' + +// Print help message if needed +if (params.help) { + def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) + def citation = '\n' + WorkflowMain.citation(workflow) + '\n' + def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" + log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) + System.exit(0) +} + +// Validate input parameters +if (params.validate_params) { + validateParameters() +} + WorkflowMain.initialise(workflow, params, log) /* diff --git a/nextflow.config b/nextflow.config index ecaa7ccb..a808d4aa 100644 --- a/nextflow.config +++ b/nextflow.config @@ -61,7 +61,6 @@ params { // Boilerplate options outdir = null - tracedir = "${params.outdir}/pipeline_info" publish_dir_mode = 'copy' email = null email_on_fail = null @@ -70,10 +69,6 @@ params { hook_url = null help = false version = false - validate_params = true - show_hidden_params = false - schema_ignore_params = 'genomes' - // Config options custom_config_version = 'master' @@ -89,6 +84,20 @@ params { max_cpus = 16 max_time = '240.h' + // Schema validation default options + validationFailUnrecognisedParams = false + validationLenientMode = false + validationSchemaIgnoreParams = 'genomes' + validationShowHiddenParams = false + validate_params = true + + // Schema validation default options + validationFailUnrecognisedParams = false + validationLenientMode = false + validationSchemaIgnoreParams = 'genomes' + validationShowHiddenParams = false + validate_params = true + } // Load base.config by default for all pipelines @@ -204,6 +213,19 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } +// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + +// Nextflow plugins +plugins { + id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} + // Load igenomes.config if required if (!params.igenomes_ignore) { includeConfig 'conf/igenomes.config' @@ -234,19 +256,19 @@ podman.registry = 'quay.io' def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" } report { enabled = true - file = "${params.tracedir}/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" } trace { enabled = true - file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" } dag { enabled = true - file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" } manifest { @@ -255,7 +277,7 @@ manifest { homePage = 'https://github.com/nf-core/smrnaseq' description = """Small RNA-Seq Best Practice Analysis Pipeline.""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' + nextflowVersion = '!>=23.04.0' version = '2.2.2' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 213199c1..331a41b6 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,9 +15,9 @@ "input": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", - "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/smrnaseq/usage#samplesheet-input).", "fa_icon": "fas fa-file-csv" @@ -80,6 +80,8 @@ }, "fasta": { "type": "string", + "format": "file-path", + "exists": true, "fa_icon": "fas fa-font", "description": "Path to reference genome FASTA genome file.", "help_text": "If you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible." @@ -348,7 +350,7 @@ "description": "Maximum amount of time that can be requested for any single job.", "default": "240.h", "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$", + "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", "hidden": true, "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" } @@ -365,12 +367,14 @@ "type": "boolean", "description": "Display help text.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "version": { "type": "boolean", "description": "Display version and exit.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "publish_dir_mode": { @@ -394,6 +398,7 @@ "type": "boolean", "description": "Send plain-text email instead of HTML.", "fa_icon": "fas fa-remove-format", + "default": false, "hidden": true }, "max_multiqc_email_size": { @@ -408,6 +413,7 @@ "type": "boolean", "description": "Do not use coloured log outputs.", "fa_icon": "fas fa-palette", + "default": false, "hidden": true }, "hook_url": { @@ -419,6 +425,7 @@ }, "multiqc_config": { "type": "string", + "format": "file-path", "description": "Custom config file to supply to MultiQC.", "fa_icon": "fas fa-cog", "hidden": true @@ -434,13 +441,6 @@ "description": "Custom MultiQC yaml file containing HTML including a methods description.", "fa_icon": "fas fa-cog" }, - "tracedir": { - "type": "string", - "description": "Directory to keep pipeline Nextflow logs and reports.", - "default": "${params.outdir}/pipeline_info", - "fa_icon": "fas fa-cogs", - "hidden": true - }, "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", @@ -448,12 +448,29 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "show_hidden_params": { + "validationShowHiddenParams": { "type": "boolean", "fa_icon": "far fa-eye-slash", "description": "Show all params when using `--help`", + "default": false, "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." + }, + "validationFailUnrecognisedParams": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters fails when an unrecognised parameter is found.", + "default": false, + "hidden": true, + "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." + }, + "validationLenientMode": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters in lenient more.", + "default": false, + "hidden": true, + "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." } } } diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf index ad5ecfef..ac9d1646 100644 --- a/workflows/smrnaseq.nf +++ b/workflows/smrnaseq.nf @@ -1,12 +1,18 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE INPUTS + PRINT PARAMS SUMMARY ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) +include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' + +def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) +def citation = '\n' + WorkflowMain.citation(workflow) + '\n' +def summary_params = paramsSummaryMap(workflow) + +// Print parameter summary log to screen +log.info logo + paramsSummaryLog(workflow) + citation -// Validate input parameters WorkflowSmrnaseq.initialise(params, log) // Check input path parameters to see if they exist @@ -96,7 +102,7 @@ workflow SMRNASEQ { // SUBWORKFLOW: Read in samplesheet, validate and stage input files // INPUT_CHECK ( - ch_input + file(params.input) ) .reads .dump(tag: 'group') @@ -109,6 +115,9 @@ workflow SMRNASEQ { } .set { ch_fastq } ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) + // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") + // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ + // ! There is currently no tooling to help you write a sample sheet schema // // MODULE: Concatenate FastQ files from same sample if required From 6223c35a9cbe37f5f4e90a7d465d5c955a84b19f Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 30 Aug 2023 06:57:33 +0000 Subject: [PATCH 12/33] Modules updates --- modules.json | 16 ++++++++-------- modules/local/mirtop_quant.nf | 4 ++-- modules/local/samplesheet_check.nf | 1 - .../nf-core/custom/dumpsoftwareversions/main.nf | 6 +++--- modules/nf-core/fastp/main.nf | 6 +++--- modules/nf-core/fastqc/main.nf | 6 +++++- modules/nf-core/multiqc/main.nf | 6 +++--- modules/nf-core/samtools/flagstat/main.nf | 11 +++++++++++ modules/nf-core/samtools/idxstats/main.nf | 12 ++++++++++++ modules/nf-core/samtools/sort/main.nf | 2 -- modules/nf-core/samtools/stats/main.nf | 2 +- modules/nf-core/samtools/stats/meta.yml | 10 ++++++++-- 12 files changed, 56 insertions(+), 26 deletions(-) diff --git a/modules.json b/modules.json index 0b6daac5..defa77af 100644 --- a/modules.json +++ b/modules.json @@ -12,32 +12,32 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", "installed_by": ["modules"] }, "fastp": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c", "installed_by": ["modules"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639", "installed_by": ["modules"] }, "samtools/index": { @@ -47,12 +47,12 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9", "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", "installed_by": ["modules"] } } diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf index 3ebb65ac..cc8d29a7 100644 --- a/modules/local/mirtop_quant.nf +++ b/modules/local/mirtop_quant.nf @@ -12,9 +12,9 @@ process MIRTOP_QUANT { path gtf output: - path "mirtop/mirtop.gff" + path "mirtop/mirtop.gff" , emit: mirtop_gff path "mirtop/mirtop.tsv" , emit: mirtop_table - path "mirtop/mirtop_rawData.tsv" + path "mirtop/mirtop_rawData.tsv", emit: mirtop_rawdata path "mirtop/stats/*" , emit: logs path "versions.yml" , emit: versions diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index c1b0967f..351d2322 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -1,5 +1,4 @@ process SAMPLESHEET_CHECK { - label 'process_low' tag "$samplesheet" label 'process_single' diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc87273..c9d014b1 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - '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/fastp/main.nf b/modules/nf-core/fastp/main.nf index 2ca2d3ee..831b7f12 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -2,10 +2,10 @@ process FASTP { tag "$meta.id" label 'process_medium' - conda "bioconda::fastp=0.23.2" + conda "bioconda::fastp=0.23.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' : - 'biocontainers/fastp:0.23.2--h79da9fb_0' }" + 'https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0' : + 'biocontainers/fastp:0.23.4--h5f740d0_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 07d5e433..249f9064 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -29,7 +29,11 @@ process FASTQC { 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 + + fastqc \\ + $args \\ + --threads $task.cpus \\ + $renamed_files cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1fc387be..65d7dd0d 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index eb7e72fc..b75707ec 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -32,4 +32,15 @@ process SAMTOOLS_FLAGSTAT { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.flagstat + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index a257d700..83c7c34b 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -33,4 +33,16 @@ process SAMTOOLS_IDXSTATS { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.idxstats + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 1e5181d4..2b7753fd 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -21,13 +21,11 @@ process SAMTOOLS_SORT { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def sort_memory = (task.memory.mega/task.cpus).intValue() if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ samtools sort \\ $args \\ -@ $task.cpus \\ - -m ${sort_memory}M \\ -o ${prefix}.bam \\ -T $prefix \\ $bam diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index eb7f098b..4a2607de 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -9,7 +9,7 @@ process SAMTOOLS_STATS { input: tuple val(meta), path(input), path(input_index) - path fasta + tuple val(meta2), path(fasta) output: tuple val(meta), path("*.stats"), emit: stats diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index 1d68a5d8..90e6345f 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -30,9 +30,14 @@ input: type: file description: BAI/CRAI file from alignment pattern: "*.{bai,crai}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - 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}" output: - meta: @@ -51,3 +56,4 @@ output: authors: - "@drpatelh" - "@FriederikeHanssen" + - "@ramprasadn" From e3867b016b0ecc7472a1c9230ec4162b9793df35 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 30 Aug 2023 07:21:05 +0000 Subject: [PATCH 13/33] Fixing merge issue --- workflows/smrnaseq.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf index ac9d1646..3489b83c 100644 --- a/workflows/smrnaseq.nf +++ b/workflows/smrnaseq.nf @@ -220,7 +220,7 @@ workflow SMRNASEQ { if (!params.skip_multiqc) { workflow_summary = WorkflowSmrnaseq.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) - methods_description = WorkflowSmrnaseq.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + methods_description = WorkflowSmrnaseq.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) ch_methods_description = Channel.value(methods_description) ch_multiqc_files = Channel.empty() From 75f4c301f40d8bf21a984ef3b92451fe929429e8 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 30 Aug 2023 07:26:19 +0000 Subject: [PATCH 14/33] 2.2.1dev --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index a808d4aa..5ac1c01e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -278,7 +278,7 @@ manifest { description = """Small RNA-Seq Best Practice Analysis Pipeline.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.2.2' + version = '2.2.1dev' doi = '' } From 157e6d89d09198926366855c7b02ea0828314ba5 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 30 Aug 2023 07:30:04 +0000 Subject: [PATCH 15/33] 2.2.1dev --- README.md | 18 ------------------ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 3 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index 24226773..7bab3d6b 100644 --- a/README.md +++ b/README.md @@ -57,26 +57,8 @@ You can find numerous talks on the nf-core events page from various topics inclu > 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. - - Now, you can run the pipeline using: - - ```bash nextflow run nf-core/smrnaseq \ -profile \ diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 23da1135..7c483b48 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/smrnaseq + This report has been generated by the nf-core/smrnaseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-smrnaseq-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 5ac1c01e..62c608b1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -278,7 +278,7 @@ manifest { description = """Small RNA-Seq Best Practice Analysis Pipeline.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.2.1dev' + version = '2.2.1dev' doi = '' } From 86a5047c7431e6cff574996d4e173dd4c97a5cb9 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 30 Aug 2023 09:50:52 +0200 Subject: [PATCH 16/33] Apply suggestions from code review Co-authored-by: Gregor Sturm --- nextflow.config | 6 ------ 1 file changed, 6 deletions(-) diff --git a/nextflow.config b/nextflow.config index 62c608b1..10181292 100644 --- a/nextflow.config +++ b/nextflow.config @@ -84,12 +84,6 @@ params { max_cpus = 16 max_time = '240.h' - // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes' - validationShowHiddenParams = false - validate_params = true // Schema validation default options validationFailUnrecognisedParams = false From 6b7d36c4adf9f5f8f1109f1fb5c5f186cf8fc868 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 30 Aug 2023 07:51:07 +0000 Subject: [PATCH 17/33] Adjust based on review --- README.md | 26 +++++++++++++++++++++----- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 24 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 7bab3d6b..005775f2 100644 --- a/README.md +++ b/README.md @@ -57,16 +57,32 @@ You can find numerous talks on the nf-core events page from various topics inclu > 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. +First, prepare a samplesheet with your input data that looks as follows: + +`samplesheet.csv`: +```csv +sample,fastq_1 +Clone1_N1,s3://ngi-igenomes/test-data/smrnaseq/C1-N1-R1_S4_L001_R1_001.fastq.gz +Clone1_N3,s3://ngi-igenomes/test-data/smrnaseq/C1-N3-R1_S6_L001_R1_001.fastq.gz +Clone9_N1,s3://ngi-igenomes/test-data/smrnaseq/C9-N1-R1_S7_L001_R1_001.fastq.gz +Clone9_N2,s3://ngi-igenomes/test-data/smrnaseq/C9-N2-R1_S8_L001_R1_001.fastq.gz +Clone9_N3,s3://ngi-igenomes/test-data/smrnaseq/C9-N3-R1_S9_L001_R1_001.fastq.gz +Control_N1,s3://ngi-igenomes/test-data/smrnaseq/Ctl-N1-R1_S1_L001_R1_001.fastq.gz +Control_N2,s3://ngi-igenomes/test-data/smrnaseq/Ctl-N2-R1_S2_L001_R1_001.fastq.gz +Control_N3,s3://ngi-igenomes/test-data/smrnaseq/Ctl-N3-R1_S3_L001_R1_001.fastq.gz +``` +Each row represents a fastq file (single-end). + Now, you can run the pipeline using: ```bash nextflow run nf-core/smrnaseq \ -profile \ - --input samplesheet.csv \ - --genome 'GRCh37' \ - --mirtrace_species 'hsa' \ - --protocol 'illumina' \ - --outdir + --input samplesheet.csv \ + --genome 'GRCh37' \ + --mirtrace_species 'hsa' \ + --protocol 'illumina' \ + --outdir ``` > **Warning:** diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 7c483b48..fe2c8740 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/smrnaseq + This report has been generated by the nf-core/smrnaseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-smrnaseq-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 62c608b1..6d12aa98 100644 --- a/nextflow.config +++ b/nextflow.config @@ -278,7 +278,7 @@ manifest { description = """Small RNA-Seq Best Practice Analysis Pipeline.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.2.1dev' + version = '2.2.2dev' doi = '' } From 845832b5a40a34c7bcbe4f4ca4df1a88d9b579dc Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 30 Aug 2023 07:52:08 +0000 Subject: [PATCH 18/33] Prettier --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 005775f2..44066051 100644 --- a/README.md +++ b/README.md @@ -60,6 +60,7 @@ You can find numerous talks on the nf-core events page from various topics inclu First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: + ```csv sample,fastq_1 Clone1_N1,s3://ngi-igenomes/test-data/smrnaseq/C1-N1-R1_S4_L001_R1_001.fastq.gz @@ -71,6 +72,7 @@ Control_N1,s3://ngi-igenomes/test-data/smrnaseq/Ctl-N1-R1_S1_L001_R1_001.fastq.g Control_N2,s3://ngi-igenomes/test-data/smrnaseq/Ctl-N2-R1_S2_L001_R1_001.fastq.gz Control_N3,s3://ngi-igenomes/test-data/smrnaseq/Ctl-N3-R1_S3_L001_R1_001.fastq.gz ``` + Each row represents a fastq file (single-end). Now, you can run the pipeline using: From 9a46d676df47c481e69c2204411fe452cb7b277f Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 30 Aug 2023 10:50:07 +0000 Subject: [PATCH 19/33] Update imported nf-core workflows --- modules.json | 24 +++++-- .../main.nf} | 15 +++-- .../nf-core/bam_sort_stats_samtools/meta.yml | 67 +++++++++++++++++++ subworkflows/nf-core/bam_stats_samtools.nf | 32 --------- .../nf-core/bam_stats_samtools/main.nf | 32 +++++++++ .../nf-core/bam_stats_samtools/meta.yml | 41 ++++++++++++ 6 files changed, 167 insertions(+), 44 deletions(-) rename subworkflows/nf-core/{bam_sort_samtools.nf => bam_sort_stats_samtools/main.nf} (77%) create mode 100644 subworkflows/nf-core/bam_sort_stats_samtools/meta.yml delete mode 100644 subworkflows/nf-core/bam_stats_samtools.nf create mode 100644 subworkflows/nf-core/bam_stats_samtools/main.nf create mode 100644 subworkflows/nf-core/bam_stats_samtools/meta.yml diff --git a/modules.json b/modules.json index defa77af..758f1b84 100644 --- a/modules.json +++ b/modules.json @@ -33,27 +33,41 @@ "samtools/flagstat": { "branch": "master", "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c", - "installed_by": ["modules"] + "installed_by": ["bam_stats_samtools", "modules"] }, "samtools/idxstats": { "branch": "master", "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639", - "installed_by": ["modules"] + "installed_by": ["bam_stats_samtools", "modules"] }, "samtools/index": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["modules"] + "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/sort": { "branch": "master", "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9", - "installed_by": ["modules"] + "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/stats": { "branch": "master", "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", - "installed_by": ["modules"] + "installed_by": ["bam_stats_samtools", "modules"] + } + } + }, + "subworkflows": { + "nf-core": { + "bam_sort_stats_samtools": { + "branch": "master", + "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", + "installed_by": ["subworkflows"] + }, + "bam_stats_samtools": { + "branch": "master", + "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", + "installed_by": ["subworkflows", "bam_sort_stats_samtools"] } } } diff --git a/subworkflows/nf-core/bam_sort_samtools.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf similarity index 77% rename from subworkflows/nf-core/bam_sort_samtools.nf rename to subworkflows/nf-core/bam_sort_stats_samtools/main.nf index ded07b32..fc1c652b 100644 --- a/subworkflows/nf-core/bam_sort_samtools.nf +++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf @@ -2,16 +2,17 @@ // Sort, index BAM file and run samtools stats, flagstat and idxstats // -include { SAMTOOLS_SORT } from '../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' -include { BAM_STATS_SAMTOOLS } from './bam_stats_samtools' +include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' +include { BAM_STATS_SAMTOOLS } from '../bam_stats_samtools/main' -workflow BAM_SORT_SAMTOOLS { +workflow BAM_SORT_STATS_SAMTOOLS { take: - ch_bam // channel: [ val(meta), [ bam ] ] - fasta + ch_bam // channel: [ val(meta), [ bam ] ] + ch_fasta // channel: [ val(meta), path(fasta) ] main: + ch_versions = Channel.empty() SAMTOOLS_SORT ( ch_bam ) @@ -33,7 +34,7 @@ workflow BAM_SORT_SAMTOOLS { } .set { ch_bam_bai } - BAM_STATS_SAMTOOLS ( ch_bam_bai, fasta ) + BAM_STATS_SAMTOOLS ( ch_bam_bai, ch_fasta ) ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions) emit: diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml new file mode 100644 index 00000000..69c16be4 --- /dev/null +++ b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml @@ -0,0 +1,67 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: bam_sort_stats_samtools +description: Sort SAM/BAM/CRAM file +keywords: + - sort + - bam + - sam + - cram +components: + - samtools/sort + - samtools/index + - samtools/stats + - samtools/idxstats + - samtools/flagstat + - bam_stats_samtools +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - fasta: + type: file + description: Reference genome fasta file + pattern: "*.{fasta,fa}" +# TODO Update when we decide on a standard for subworkflow docs +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - crai: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - stats: + type: file + description: File containing samtools stats output + pattern: "*.{stats}" + - flagstat: + type: file + description: File containing samtools flagstat output + pattern: "*.{flagstat}" + - idxstats: + type: file + description: File containing samtools idxstats output + pattern: "*.{idxstats}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@ewels" diff --git a/subworkflows/nf-core/bam_stats_samtools.nf b/subworkflows/nf-core/bam_stats_samtools.nf deleted file mode 100644 index 38d2569b..00000000 --- a/subworkflows/nf-core/bam_stats_samtools.nf +++ /dev/null @@ -1,32 +0,0 @@ -// -// Run SAMtools stats, flagstat and idxstats -// - -include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main' -include { SAMTOOLS_IDXSTATS } from '../../modules/nf-core/samtools/idxstats/main' -include { SAMTOOLS_FLAGSTAT } from '../../modules/nf-core/samtools/flagstat/main' - -workflow BAM_STATS_SAMTOOLS { - take: - ch_bam_bai // channel: [ val(meta), [ bam ], [bai/csi] ] - fasta - - main: - ch_versions = Channel.empty() - - SAMTOOLS_STATS ( ch_bam_bai, fasta ) - ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first()) - - SAMTOOLS_FLAGSTAT ( ch_bam_bai ) - ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions.first()) - - SAMTOOLS_IDXSTATS ( ch_bam_bai ) - ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions.first()) - - emit: - stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), [ stats ] ] - flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), [ flagstat ] ] - idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), [ idxstats ] ] - - versions = ch_versions // channel: [ versions.yml ] -} diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf new file mode 100644 index 00000000..44d4c010 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/main.nf @@ -0,0 +1,32 @@ +// +// Run SAMtools stats, flagstat and idxstats +// + +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' +include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main' +include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' + +workflow BAM_STATS_SAMTOOLS { + take: + ch_bam_bai // channel: [ val(meta), path(bam), path(bai) ] + ch_fasta // channel: [ val(meta), path(fasta) ] + + main: + ch_versions = Channel.empty() + + SAMTOOLS_STATS ( ch_bam_bai, ch_fasta ) + ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) + + SAMTOOLS_FLAGSTAT ( ch_bam_bai ) + ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions) + + SAMTOOLS_IDXSTATS ( ch_bam_bai ) + ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions) + + emit: + stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] + flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), path(flagstat) ] + idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), path(idxstats) ] + + versions = ch_versions // channel: [ path(versions.yml) ] +} diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml new file mode 100644 index 00000000..87863b11 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/meta.yml @@ -0,0 +1,41 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: bam_stats_samtools +description: Produces comprehensive statistics from SAM/BAM/CRAM file +keywords: + - statistics + - counts + - bam + - sam + - cram +components: + - samtools/stats + - samtools/idxstats + - samtools/flagstat +input: + - ch_bam_bai: + description: | + The input channel containing the BAM/CRAM and it's index + Structure: [ val(meta), path(bam), path(bai) ] + - ch_fasta: + description: | + Reference genome fasta file + Structure: [ path(fasta) ] +output: + - stats: + description: | + File containing samtools stats output + Structure: [ val(meta), path(stats) ] + - flagstat: + description: | + File containing samtools flagstat output + Structure: [ val(meta), path(flagstat) ] + - idxstats: + description: | + File containing samtools idxstats output + Structure: [ val(meta), path(idxstats)] + - versions: + description: | + Files containing software versions + Structure: [ path(versions.yml) ] +authors: + - "@drpatelh" From cbebb5a824849620b0c4836bcb069b08f8774ba7 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 30 Aug 2023 10:56:19 +0000 Subject: [PATCH 20/33] Update workflows with nf-core ones --- subworkflows/local/genome_quant.nf | 8 ++++---- subworkflows/local/mirna_quant.nf | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/genome_quant.nf b/subworkflows/local/genome_quant.nf index 033f59ad..a20a7c1f 100644 --- a/subworkflows/local/genome_quant.nf +++ b/subworkflows/local/genome_quant.nf @@ -3,7 +3,7 @@ // include { INDEX_GENOME } from '../../modules/local/bowtie_genome' -include { BAM_SORT_SAMTOOLS } from '../nf-core/bam_sort_samtools' +include { BAM_SORT_STATS_SAMTOOLS } from '../nf-core/bam_sort_stats_samtools' include { BOWTIE_MAP_SEQ as BOWTIE_MAP_GENOME } from '../../modules/local/bowtie_map_mirna' workflow GENOME_QUANT { @@ -29,14 +29,14 @@ workflow GENOME_QUANT { BOWTIE_MAP_GENOME ( reads, bowtie_index.collect() ) ch_versions = ch_versions.mix(BOWTIE_MAP_GENOME.out.versions) - BAM_SORT_SAMTOOLS ( BOWTIE_MAP_GENOME.out.bam, Channel.empty() ) - ch_versions = ch_versions.mix(BAM_SORT_SAMTOOLS.out.versions) + BAM_SORT_STATS_SAMTOOLS ( BOWTIE_MAP_GENOME.out.bam, Channel.empty() ) + ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions) } emit: fasta = fasta_formatted index = bowtie_index - stats = BAM_SORT_SAMTOOLS.out.stats + stats = BAM_SORT_STATS_SAMTOOLS.out.stats versions = ch_versions } diff --git a/subworkflows/local/mirna_quant.nf b/subworkflows/local/mirna_quant.nf index dd8a8412..70b872e3 100644 --- a/subworkflows/local/mirna_quant.nf +++ b/subworkflows/local/mirna_quant.nf @@ -15,8 +15,8 @@ include { BOWTIE_MAP_SEQ as BOWTIE_MAP_MATURE BOWTIE_MAP_SEQ as BOWTIE_MAP_HAIRPIN BOWTIE_MAP_SEQ as BOWTIE_MAP_SEQCLUSTER } from '../../modules/local/bowtie_map_mirna' -include { BAM_SORT_SAMTOOLS as BAM_STATS_MATURE - BAM_SORT_SAMTOOLS as BAM_STATS_HAIRPIN } from '../nf-core/bam_sort_samtools' +include { BAM_SORT_STATS_SAMTOOLS as BAM_STATS_MATURE + BAM_SORT_STATS_SAMTOOLS as BAM_STATS_HAIRPIN } from '../nf-core/bam_sort_stats_samtools' include { SEQCLUSTER_SEQUENCES } from '../../modules/local/seqcluster_collapse.nf' include { MIRTOP_QUANT } from '../../modules/local/mirtop_quant.nf' From 37f85f790caf26dfa833639e919361e1a3ecb9ac Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 30 Aug 2023 11:43:00 +0000 Subject: [PATCH 21/33] Fix prefix --- conf/modules.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 8644dd3c..556d8509 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -207,7 +207,7 @@ process { } process { - withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_SAMTOOLS:SAMTOOLS_.*' { + withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_.*' { ext.prefix = { "${meta.id}.sorted" } publishDir = [ path: { "${params.outdir}/samtools" }, @@ -215,7 +215,7 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } - withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' { + withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' { ext.prefix = { "${meta.id}.sorted" } publishDir = [ path: { "${params.outdir}/samtools/samtools_stats" }, From ec610e6d0a5ecdddc0bd53fafe6d0c14aac56832 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 1 Sep 2023 07:09:47 +0000 Subject: [PATCH 22/33] Attempt at introducing meta2 everywhere --- modules/local/bowtie_genome.nf | 2 +- modules/local/bowtie_mirna.nf | 2 +- modules/local/format_fasta_mirna.nf | 4 ++-- modules/local/mirdeep2_run.nf | 2 +- modules/local/parse_fasta_mirna.nf | 2 +- subworkflows/local/genome_quant.nf | 2 +- 6 files changed, 7 insertions(+), 7 deletions(-) diff --git a/modules/local/bowtie_genome.nf b/modules/local/bowtie_genome.nf index b132e1da..91a6cd53 100644 --- a/modules/local/bowtie_genome.nf +++ b/modules/local/bowtie_genome.nf @@ -8,7 +8,7 @@ process INDEX_GENOME { 'biocontainers/bowtie:1.3.1--py310h4070885_4' }" input: - path fasta + tuple val(meta2), path(fasta) output: path 'genome*ebwt' , emit: index diff --git a/modules/local/bowtie_mirna.nf b/modules/local/bowtie_mirna.nf index 9390730a..2be45bb8 100644 --- a/modules/local/bowtie_mirna.nf +++ b/modules/local/bowtie_mirna.nf @@ -7,7 +7,7 @@ process INDEX_MIRNA { 'biocontainers/bowtie:1.3.1--py310h4070885_4' }" input: - path fasta + tuple val(meta2), path(fasta) output: path 'fasta_bidx*' , emit: index diff --git a/modules/local/format_fasta_mirna.nf b/modules/local/format_fasta_mirna.nf index 3e247ce4..637a6604 100644 --- a/modules/local/format_fasta_mirna.nf +++ b/modules/local/format_fasta_mirna.nf @@ -10,10 +10,10 @@ process FORMAT_FASTA_MIRNA { 'biocontainers/fastx_toolkit:0.0.14--he1b5a44_8' }" input: - path fasta + tuple val(meta2), path(fasta) output: - path '*_idx.fa' , emit: formatted_fasta + tuple meta2, path '*_idx.fa' , emit: formatted_fasta path "versions.yml", emit: versions when: diff --git a/modules/local/mirdeep2_run.nf b/modules/local/mirdeep2_run.nf index 74044e4a..e4e2aaaf 100644 --- a/modules/local/mirdeep2_run.nf +++ b/modules/local/mirdeep2_run.nf @@ -10,7 +10,7 @@ process MIRDEEP2_RUN { 'biocontainers/mirdeep2:2.0.1.3--hdfd78af_1' }" input: - path fasta + tuple val(meta2), path(fasta) tuple path(reads), path(arf) path hairpin path mature diff --git a/modules/local/parse_fasta_mirna.nf b/modules/local/parse_fasta_mirna.nf index ab7a91f0..22950833 100644 --- a/modules/local/parse_fasta_mirna.nf +++ b/modules/local/parse_fasta_mirna.nf @@ -7,7 +7,7 @@ process PARSE_FASTA_MIRNA { 'biocontainers/seqkit:2.3.1--h9ee0642_0' }" input: - path fasta + tuple val(meta2), path(fasta) output: path '*_igenome.fa', emit: parsed_fasta diff --git a/subworkflows/local/genome_quant.nf b/subworkflows/local/genome_quant.nf index a20a7c1f..39d17e8a 100644 --- a/subworkflows/local/genome_quant.nf +++ b/subworkflows/local/genome_quant.nf @@ -8,7 +8,7 @@ include { BOWTIE_MAP_SEQ as BOWTIE_MAP_GENOME } from '../../modules/local/bowtie workflow GENOME_QUANT { take: - fasta + fasta //channel: [ val(meta2), [ reads ] ] index reads // channel: [ val(meta), [ reads ] ] From 26f95a119940c4348245ada3a501e9bf523fe46b Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 1 Sep 2023 09:19:07 +0200 Subject: [PATCH 23/33] Update modules/local/format_fasta_mirna.nf Co-authored-by: Christopher Mohr --- modules/local/format_fasta_mirna.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/format_fasta_mirna.nf b/modules/local/format_fasta_mirna.nf index 637a6604..c2efca97 100644 --- a/modules/local/format_fasta_mirna.nf +++ b/modules/local/format_fasta_mirna.nf @@ -13,7 +13,7 @@ process FORMAT_FASTA_MIRNA { tuple val(meta2), path(fasta) output: - tuple meta2, path '*_idx.fa' , emit: formatted_fasta + tuple val(meta2), path('*_idx.fa') , emit: formatted_fasta path "versions.yml", emit: versions when: From cd6c2ab3bbd004f50bfc71b1d6bddc4d8c22fe4a Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 1 Sep 2023 07:49:56 +0000 Subject: [PATCH 24/33] Add chanel description --- subworkflows/local/mirna_quant.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/mirna_quant.nf b/subworkflows/local/mirna_quant.nf index 70b872e3..b1904296 100644 --- a/subworkflows/local/mirna_quant.nf +++ b/subworkflows/local/mirna_quant.nf @@ -25,8 +25,8 @@ include { EDGER_QC } from '../../modules/local/edger_qc.nf' workflow MIRNA_QUANT { take: - mature // channel: fasta file - hairpin // channel: fasta file + mature // channel: [ val(meta), fasta file] + hairpin // channel: [ val(meta), fasta file] gtf // channle: GTF file reads // channel: [ val(meta), [ reads ] ] From ea6b8e61c7172844f09534484936f7490ae9b367 Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Fri, 1 Sep 2023 09:33:08 +0000 Subject: [PATCH 25/33] adapt fasta channel of modules and subworkflows --- modules/local/format_fasta_mirna.nf | 4 ++-- modules/local/parse_fasta_mirna.nf | 4 ++-- subworkflows/local/genome_quant.nf | 2 +- subworkflows/local/mirna_quant.nf | 2 +- workflows/smrnaseq.nf | 4 ++-- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/modules/local/format_fasta_mirna.nf b/modules/local/format_fasta_mirna.nf index c2efca97..489879a5 100644 --- a/modules/local/format_fasta_mirna.nf +++ b/modules/local/format_fasta_mirna.nf @@ -13,8 +13,8 @@ process FORMAT_FASTA_MIRNA { tuple val(meta2), path(fasta) output: - tuple val(meta2), path('*_idx.fa') , emit: formatted_fasta - path "versions.yml", emit: versions + tuple val(meta2), path('*_idx.fa') , emit: formatted_fasta + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/parse_fasta_mirna.nf b/modules/local/parse_fasta_mirna.nf index 22950833..71f5c85a 100644 --- a/modules/local/parse_fasta_mirna.nf +++ b/modules/local/parse_fasta_mirna.nf @@ -10,8 +10,8 @@ process PARSE_FASTA_MIRNA { tuple val(meta2), path(fasta) output: - path '*_igenome.fa', emit: parsed_fasta - path "versions.yml", emit: versions + tuple val(meta2), path('*_igenome.fa'), emit: parsed_fasta + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/subworkflows/local/genome_quant.nf b/subworkflows/local/genome_quant.nf index 39d17e8a..07f4fa53 100644 --- a/subworkflows/local/genome_quant.nf +++ b/subworkflows/local/genome_quant.nf @@ -16,7 +16,7 @@ workflow GENOME_QUANT { ch_versions = Channel.empty() if (!index){ - INDEX_GENOME ( fasta ) + INDEX_GENOME ( [ [:], fasta ] ) bowtie_index = INDEX_GENOME.out.index fasta_formatted = INDEX_GENOME.out.fasta ch_versions = ch_versions.mix(INDEX_GENOME.out.versions) diff --git a/subworkflows/local/mirna_quant.nf b/subworkflows/local/mirna_quant.nf index b1904296..dfa16ab4 100644 --- a/subworkflows/local/mirna_quant.nf +++ b/subworkflows/local/mirna_quant.nf @@ -94,7 +94,7 @@ workflow MIRNA_QUANT { ch_mirtop_logs = Channel.empty() if (params.mirtrace_species){ - MIRTOP_QUANT ( BOWTIE_MAP_SEQCLUSTER.out.bam.collect{it[1]}, FORMAT_HAIRPIN.out.formatted_fasta, gtf ) + MIRTOP_QUANT ( BOWTIE_MAP_SEQCLUSTER.out.bam.collect{it[1]}, FORMAT_HAIRPIN.out.formatted_fasta.collect{it[1]}, gtf ) ch_mirtop_logs = MIRTOP_QUANT.out.logs ch_versions = ch_versions.mix(MIRTOP_QUANT.out.versions) diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf index 3489b83c..cce83e56 100644 --- a/workflows/smrnaseq.nf +++ b/workflows/smrnaseq.nf @@ -179,8 +179,8 @@ workflow SMRNASEQ { } MIRNA_QUANT ( - reference_mature, - reference_hairpin, + [ [:], reference_mature], + [ [:], reference_hairpin], mirna_gtf, mirna_reads ) From a026ba147e10833d46968b1b49a291ae3deb0817 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 1 Sep 2023 11:47:08 +0000 Subject: [PATCH 26/33] Fix adapter trim for illumina case --- CHANGELOG.md | 1 + lib/WorkflowSmrnaseq.groovy | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2ca1a1cc..c9ce51eb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [v2.2.2](https://github.com/nf-core/smrnaseq/releases/tag/2.2.2) - 2023-06-01 - [[#253]](https://github.com/nf-core/smrnaseq/pull/253) - Remove globs from process alias when using ECR containers +- [[#237]](https://github.com/nf-core/smrnaseq/issues/237) - Fix illumina protocol clip parameters to default ## [v2.2.1](https://github.com/nf-core/smrnaseq/releases/tag/2.2.1) - 2023-05-12 diff --git a/lib/WorkflowSmrnaseq.groovy b/lib/WorkflowSmrnaseq.groovy index 703c1342..5b94bad7 100755 --- a/lib/WorkflowSmrnaseq.groovy +++ b/lib/WorkflowSmrnaseq.groovy @@ -125,8 +125,8 @@ class WorkflowSmrnaseq { switch(params.protocol){ case 'illumina': - params.putIfAbsent("clip_r1", 1); - params.putIfAbsent("three_prime_clip_r1",2); + params.putIfAbsent("clip_r1", 0); + params.putIfAbsent("three_prime_clip_r1",0); params.putIfAbsent("three_prime_adapter", "TGGAATTCTCGGGTGCCAAGG"); break case 'nextflex': From 9637f9b7700a534010e7c4b55f793dc3f45e3e82 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 4 Sep 2023 11:38:53 +0200 Subject: [PATCH 27/33] Update nextflow.config Co-authored-by: Christopher Mohr --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 29d41588..ff524df5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -272,7 +272,7 @@ manifest { description = """Small RNA-Seq Best Practice Analysis Pipeline.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.2.2dev' + version = '2.2.2' doi = '' } From 83b20b2de704954f620cb734c06ee65e9ef43db7 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 4 Sep 2023 11:44:41 +0200 Subject: [PATCH 28/33] Update subworkflows/local/genome_quant.nf Co-authored-by: Christopher Mohr --- subworkflows/local/genome_quant.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/genome_quant.nf b/subworkflows/local/genome_quant.nf index 07f4fa53..edb60a2a 100644 --- a/subworkflows/local/genome_quant.nf +++ b/subworkflows/local/genome_quant.nf @@ -8,7 +8,7 @@ include { BOWTIE_MAP_SEQ as BOWTIE_MAP_GENOME } from '../../modules/local/bowtie workflow GENOME_QUANT { take: - fasta //channel: [ val(meta2), [ reads ] ] + fasta index reads // channel: [ val(meta), [ reads ] ] From 0752c18dd6cb29ce691839b953e49eec7dd01513 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 4 Sep 2023 09:49:46 +0000 Subject: [PATCH 29/33] Adjust bits from PR review --- CHANGELOG.md | 12 ++++++++---- assets/multiqc_config.yml | 4 ++-- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c9ce51eb..65e46193 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,14 +3,18 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## dev +## [v2.2.2](https://github.com/nf-core/smrnaseq/releases/tag/2.2.2) - 2023-09-04 +- [[#253]](https://github.com/nf-core/smrnaseq/pull/253) - Remove globs from process alias when using ECR containers +- [[#237]](https://github.com/nf-core/smrnaseq/issues/237) - Fix illumina protocol clip parameters to default - Remove public_aws_ecr profile -## [v2.2.2](https://github.com/nf-core/smrnaseq/releases/tag/2.2.2) - 2023-06-01 +### Software dependencies -- [[#253]](https://github.com/nf-core/smrnaseq/pull/253) - Remove globs from process alias when using ECR containers -- [[#237]](https://github.com/nf-core/smrnaseq/issues/237) - Fix illumina protocol clip parameters to default +| Dependency | Old version | New version | +| ---------- | ----------- | ----------- | +| `multiqc` | 1.13 | 1.15 | +| `fastp` | 0.23.2 | 0.23.4 | ## [v2.2.1](https://github.com/nf-core/smrnaseq/releases/tag/2.2.1) - 2023-05-12 diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index fe2c8740..23da1135 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/smrnaseq + This report has been generated by the nf-core/smrnaseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-smrnaseq-methods-description": order: -1000 From 0602c6136a8f3f18ae83dd33314d6affc749a7e3 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 4 Sep 2023 12:50:55 +0000 Subject: [PATCH 30/33] Adjust changelog [skip ci] --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 65e46193..fc874c04 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#253]](https://github.com/nf-core/smrnaseq/pull/253) - Remove globs from process alias when using ECR containers - [[#237]](https://github.com/nf-core/smrnaseq/issues/237) - Fix illumina protocol clip parameters to default - Remove public_aws_ecr profile +- [[#269]](https://github.com/nf-core/smrnaseq/pull/269) - Updated miRBase URLs with new location (old ones were broken) ### Software dependencies From c55210f92ed5d303a889595b14603692d6bedc98 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 4 Sep 2023 17:35:18 +0200 Subject: [PATCH 31/33] Update nextflow.config Bugfix for users who are running offline / with -all distribution as seen in discussion with @bentsherman https://github.com/nextflow-io/nextflow/discussions/4126 --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index ff524df5..44544307 100644 --- a/nextflow.config +++ b/nextflow.config @@ -217,7 +217,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-validation@0.3.1'// Validation of pipeline parameters and creation of an input channel from a sample sheet } // Load igenomes.config if required From 703bf6173bae08c5ea08637d36202dadc3542865 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 4 Sep 2023 15:56:45 +0000 Subject: [PATCH 32/33] Revert to latest --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 44544307..c9f81e43 100644 --- a/nextflow.config +++ b/nextflow.config @@ -217,7 +217,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-validation@0.3.1'// Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-validation'// Validation of pipeline parameters and creation of an input channel from a sample sheet } // Load igenomes.config if required From d0be63a91577f9914a0466bfa90c658a4f44f146 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 5 Sep 2023 11:14:50 +0200 Subject: [PATCH 33/33] Update genome_quant.nf [skip ci] --- subworkflows/local/genome_quant.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/genome_quant.nf b/subworkflows/local/genome_quant.nf index edb60a2a..967b2757 100644 --- a/subworkflows/local/genome_quant.nf +++ b/subworkflows/local/genome_quant.nf @@ -8,7 +8,7 @@ include { BOWTIE_MAP_SEQ as BOWTIE_MAP_GENOME } from '../../modules/local/bowtie workflow GENOME_QUANT { take: - fasta + fasta index reads // channel: [ val(meta), [ reads ] ]