run nf-core modules lint --update-meta-yml to some modules

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:

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

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"

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"