From c6c7ccba52d5431197923c21f4725ffa266670c4 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 21 Jun 2024 15:57:40 +0200 Subject: [PATCH] run nf-core modules lint --update-meta-yml to some modules --- modules/nf-core/atlas/splitmerge/meta.yml | 55 ++++++----- modules/nf-core/bwa/mem/environment.yml | 5 +- modules/nf-core/bwa/mem/meta.yml | 69 ++++++++++--- modules/nf-core/fastp/meta.yml | 98 +++++++++++++++---- modules/nf-core/multiqc/meta.yml | 43 +++++--- modules/nf-core/pear/meta.yml | 57 ++++++++--- .../nf-core/samtools/index/environment.yml | 4 +- modules/nf-core/samtools/index/meta.yml | 60 ++++++++---- modules/nf-core/samtools/sort/environment.yml | 4 +- modules/nf-core/samtools/sort/meta.yml | 64 +++++++++--- 10 files changed, 337 insertions(+), 122 deletions(-) diff --git a/modules/nf-core/atlas/splitmerge/meta.yml b/modules/nf-core/atlas/splitmerge/meta.yml index fc6289c78da4..02cacea49a4b 100644 --- a/modules/nf-core/atlas/splitmerge/meta.yml +++ b/modules/nf-core/atlas/splitmerge/meta.yml @@ -7,58 +7,59 @@ keywords: - read group tools: - "atlas": - description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity" - homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" - documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" - tool_dev_url: "https://bitbucket.org/wegmannlab/atlas" - doi: "10.1101/105346" - licence: "['GPL v3']" + description: "ATLAS, a suite of methods to accurately genotype and estimate genetic + diversity" + homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" + documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" + tool_dev_url: "https://bitbucket.org/wegmannlab/atlas" + doi: "10.1101/105346" + licence: "['GPL v3']" + identifier: biotools:atlas_db input: - - meta: + - + - meta: + qualifier: val type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - bam: + - bam: + qualifier: path type: file description: Single input BAM file. pattern: "*.bam" - - bai: + - bai: + qualifier: path type: file description: The BAI file for the input BAM file pattern: "*.bai" - - read_group_setting: - type: file - description: | - TXT file containing the split and merge settings for - each readgroup. Each line consist of one readgroup, - single/double identifier and the maximum cycle number - of the sequencer. e.g. "RG1 single 100" - pattern: "*.txt" - - blacklist: + - read_group_settings: + qualifier: path + - blacklist: + qualifier: path type: file description: | blacklist.txt (optional), A txt file with blacklisted read names that should be ignored and just written to file, each on a new line pattern: "*.txt" output: - - meta: + - data: + - meta: + qualifier: val type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + - '*_mergedReads.bam': + qualifier: path + - '*.txt.gz': + qualifier: path - versions: + - versions.yml: + qualifier: path type: file description: File containing software versions pattern: "versions.yml" - - bam: - type: file - description: A BAM file with suffix_mergedReads.bam - pattern: "*_mergedReads.bam" - - filelist: - type: file - description: A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz - pattern: "*.txt.gz" authors: - "@merszym" maintainers: diff --git a/modules/nf-core/bwa/mem/environment.yml b/modules/nf-core/bwa/mem/environment.yml index 3aa9f0cca234..719885204582 100644 --- a/modules/nf-core/bwa/mem/environment.yml +++ b/modules/nf-core/bwa/mem/environment.yml @@ -1,10 +1,11 @@ name: bwa_mem + channels: - conda-forge - bioconda - defaults + dependencies: - bwa=0.7.18 - # renovate: datasource=conda depName=bioconda/samtools - - samtools=1.20 - htslib=1.20.0 + - samtools=1.20 diff --git a/modules/nf-core/bwa/mem/meta.yml b/modules/nf-core/bwa/mem/meta.yml index b126dd86a8a2..118639d32670 100644 --- a/modules/nf-core/bwa/mem/meta.yml +++ b/modules/nf-core/bwa/mem/meta.yml @@ -10,59 +10,102 @@ keywords: - sam tools: - bwa: - description: | - BWA is a software package for mapping DNA sequences against - a large reference genome, such as the human genome. - homepage: http://bio-bwa.sourceforge.net/ - documentation: https://bio-bwa.sourceforge.net/bwa.shtml - arxiv: arXiv:1303.3997 - licence: ["GPL-3.0-or-later"] + description: | + BWA is a software package for mapping DNA sequences against + a large reference genome, such as the human genome. + homepage: http://bio-bwa.sourceforge.net/ + documentation: https://bio-bwa.sourceforge.net/bwa.shtml + arxiv: arXiv:1303.3997 + licence: ["GPL-3.0-or-later"] + identifier: '' input: - - meta: + - + - meta: + qualifier: val type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - reads: + - reads: + qualifier: path type: file description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - - meta2: + - + - meta2: + qualifier: val type: map description: | Groovy Map containing reference information. e.g. [ id:'test', single_end:false ] - - index: + - index: + qualifier: path type: file description: BWA genome index files pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" - - fasta: + - + - meta3: + qualifier: val + - fasta: + qualifier: path type: file description: Reference genome in FASTA format pattern: "*.{fasta,fa}" - - sort_bam: + - + - sort_bam: + qualifier: val type: boolean description: use samtools sort (true) or samtools view (false) pattern: "true or false" output: - bam: + - meta: + qualifier: val + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - '*.bam': + qualifier: path type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - cram: + - meta: + qualifier: val + type: file + description: Output CRAM file containing read alignments + pattern: "*.{cram}" + - '*.cram': + qualifier: path type: file description: Output CRAM file containing read alignments pattern: "*.{cram}" - csi: + - meta: + qualifier: val + type: file + description: Optional index file for BAM file + pattern: "*.{csi}" + - '*.csi': + qualifier: path type: file description: Optional index file for BAM file pattern: "*.{csi}" - crai: + - meta: + qualifier: val + type: file + description: Optional index file for CRAM file + pattern: "*.{crai}" + - '*.crai': + qualifier: path type: file description: Optional index file for CRAM file pattern: "*.{crai}" - versions: + - versions.yml: + qualifier: path type: file description: File containing software versions pattern: "versions.yml" diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml index 8dfecc1848c5..d7d4fd3886a0 100644 --- a/modules/nf-core/fastp/meta.yml +++ b/modules/nf-core/fastp/meta.yml @@ -6,71 +6,129 @@ keywords: - fastq tools: - fastp: - description: | - A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. - documentation: https://github.com/OpenGene/fastp - doi: 10.1093/bioinformatics/bty560 - licence: ["MIT"] + description: | + A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. + documentation: https://github.com/OpenGene/fastp + doi: 10.1093/bioinformatics/bty560 + licence: ["MIT"] + identifier: biotools:fastp input: - - meta: + - + - meta: + qualifier: val type: map description: | Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. e.g. [ id:'test', single_end:false ] - - reads: + - reads: + qualifier: path type: file description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. If you wish to run interleaved paired-end data, supply as single-end data but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. - - adapter_fasta: + - + - adapter_fasta: + qualifier: path type: file description: File in FASTA format containing possible adapters to remove. pattern: "*.{fasta,fna,fas,fa}" - - discard_trimmed_pass: + - + - discard_trimmed_pass: + qualifier: val type: boolean - description: Specify true to not write any reads that pass trimming thresholds. | - This can be used to use fastp for the output report only. - - save_trimmed_fail: + description: Specify true to not write any reads that pass trimming thresholds. + | This can be used to use fastp for the output report only. + - + - save_trimmed_fail: + qualifier: val type: boolean - description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz` - - save_merged: + description: Specify true to save files that failed to pass trimming thresholds + ending in `*.fail.fastq.gz` + - + - save_merged: + qualifier: val type: boolean description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` output: - - meta: + - reads: + - meta: + qualifier: val type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - reads: + - '*.fastp.fastq.gz': + qualifier: path type: file description: The trimmed/modified/unmerged fastq reads pattern: "*fastp.fastq.gz" - json: + - meta: + qualifier: val + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.json': + qualifier: path type: file description: Results in JSON format pattern: "*.json" - html: + - meta: + qualifier: val + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.html': + qualifier: path type: file description: Results in HTML format pattern: "*.html" - log: + - meta: + qualifier: val + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.log': + qualifier: path type: file description: fastq log file pattern: "*.log" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads_fail: + - meta: + qualifier: val + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.fail.fastq.gz': + qualifier: path type: file description: Reads the failed the preprocessing pattern: "*fail.fastq.gz" - reads_merged: + - meta: + qualifier: val + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.merged.fastq.gz': + qualifier: path type: file description: Reads that were successfully merged pattern: "*.{merged.fastq.gz}" + - versions: + - versions.yml: + qualifier: path + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc35e109..1607098fde67 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,48 +1,67 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools - Beautiful stand-alone HTML report tools: - multiqc: - description: | - MultiQC searches a given directory for analysis logs and compiles a HTML report. - It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. - homepage: https://multiqc.info/ - documentation: https://multiqc.info/docs/ - licence: ["GPL-3.0-or-later"] + description: | + MultiQC searches a given directory for analysis logs and compiles a HTML report. + It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + homepage: https://multiqc.info/ + documentation: https://multiqc.info/docs/ + licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: + - + - multiqc_files: + qualifier: path type: file description: | List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: + - + - multiqc_config: + qualifier: path type: file description: Optional config yml for MultiQC pattern: "*.{yml,yaml}" - - extra_multiqc_config: + - + - extra_multiqc_config: + qualifier: path type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. pattern: "*.{yml,yaml}" - - multiqc_logo: + - + - multiqc_logo: + qualifier: path type: file description: Optional logo file for MultiQC pattern: "*.{png}" output: - report: + - '*multiqc_report.html': + qualifier: path type: file description: MultiQC report file pattern: "multiqc_report.html" - data: + - '*_data': + qualifier: path type: directory description: MultiQC data dir pattern: "multiqc_data" - plots: + - '*_plots': + qualifier: path type: file description: Plots created by MultiQC pattern: "*_data" - versions: + - versions.yml: + qualifier: path type: file description: File containing software versions pattern: "versions.yml" diff --git a/modules/nf-core/pear/meta.yml b/modules/nf-core/pear/meta.yml index 8f100600364b..2f80f4fb6113 100644 --- a/modules/nf-core/pear/meta.yml +++ b/modules/nf-core/pear/meta.yml @@ -1,47 +1,78 @@ name: "pear" -description: PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. +description: PEAR is an ultrafast, memory-efficient and highly accurate pair-end read + merger. keywords: - pair-end - read - merge tools: - "pear": - description: "paired-end read merger" - homepage: "https://cme.h-its.org/exelixis/web/software/pear/" - documentation: "https://cme.h-its.org/exelixis/web/software/pear/doc.html" - licence: ["Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported"] + description: "paired-end read merger" + homepage: "https://cme.h-its.org/exelixis/web/software/pear/" + documentation: "https://cme.h-its.org/exelixis/web/software/pear/doc.html" + licence: ["Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported"] + identifier: biotools:pear input: - - meta: + - + - meta: + qualifier: val type: map description: | Groovy Map containing sample information e.g. [ id:'test' ] - - reads: + - reads: + qualifier: path type: file description: | List of input FastQ files with paired-end reads forward and reverse. output: - - meta: + - assembled: + - meta: + qualifier: val type: map description: | Groovy Map containing sample information e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - assembled: + - '*.assembled.fastq.gz': + qualifier: path type: file description: FastQ file containing Assembled reads. pattern: "*.{fastq.gz}" - unassembled: + - meta: + qualifier: val + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - '*.unassembled.forward.fastq.gz': + qualifier: path + type: file + description: FastQ files containing Unassembled forward and reverse reads. + pattern: "*.{fastq.gz}" + - '*.unassembled.reverse.fastq.gz': + qualifier: path type: file description: FastQ files containing Unassembled forward and reverse reads. pattern: "*.{fastq.gz}" - discarded: + - meta: + qualifier: val + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - '*.discarded.fastq.gz': + qualifier: path type: file description: FastQ file containing discarded reads. pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + qualifier: path + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mirpedrol" maintainers: diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 260d516be9ff..369b58a26e70 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,8 +1,10 @@ name: samtools_index + channels: - conda-forge - bioconda - defaults + dependencies: - - bioconda::samtools=1.20 - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 01a4ee03eb9d..54056c280f18 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -7,43 +7,65 @@ keywords: - cram tools: - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: http://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ["MIT"] + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: http://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] + identifier: biotools:samtools input: - - meta: + - + - meta: + qualifier: val 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}" + - input: + qualifier: path output: - - meta: + - bai: + - meta: + qualifier: val type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - bai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - crai: + - '*.bai': + qualifier: path type: file description: BAM/CRAM/SAM index file pattern: "*.{bai,crai,sai}" - csi: + - meta: + qualifier: val + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.csi': + qualifier: path type: file description: CSI index file pattern: "*.{csi}" + - crai: + - meta: + qualifier: val + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.crai': + qualifier: path + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - versions: + - versions.yml: + qualifier: path type: file description: File containing software versions pattern: "versions.yml" diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 36a12eab0f20..af1f2cf6a943 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,8 +1,10 @@ name: samtools_sort + channels: - conda-forge - bioconda - defaults + dependencies: - - bioconda::samtools=1.20 - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 341a7d0ebf46..3d25d8f35d90 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -7,57 +7,93 @@ keywords: - cram tools: - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: http://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ["MIT"] + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: http://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] + identifier: biotools:samtools input: - - meta: + - + - meta: + qualifier: val type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - bam: + - bam: + qualifier: path type: file description: BAM/CRAM/SAM file(s) pattern: "*.{bam,cram,sam}" - - meta2: + - + - meta2: + qualifier: val type: map description: | Groovy Map containing reference information e.g. [ id:'genome' ] - - fasta: + - fasta: + qualifier: path type: file description: Reference genome FASTA file pattern: "*.{fa,fasta,fna}" optional: true output: - - meta: + - bam: + - meta: + qualifier: val type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - bam: + - '*.bam': + qualifier: path type: file description: Sorted BAM file pattern: "*.{bam}" - cram: + - meta: + qualifier: val + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.cram': + qualifier: path type: file description: Sorted CRAM file pattern: "*.{cram}" - crai: + - meta: + qualifier: val + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.crai': + qualifier: path type: file description: CRAM index file (optional) pattern: "*.crai" - csi: + - meta: + qualifier: val + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.csi': + qualifier: path type: file description: BAM index file (optional) pattern: "*.csi" - versions: + - versions.yml: + qualifier: path type: file description: File containing software versions pattern: "versions.yml"