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

modules/nf-core/atlas/splitmerge/meta.yml

@@ -7,58 +7,71 @@ keywords:
   - read group
 tools:
   - "atlas":
-      description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
+      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']"
+      licence: ["GPL v3"]
+      identifier: biotools:atlas_db
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - bam:
-      type: file
-      description: Single input BAM file.
-      pattern: "*.bam"
-  - bai:
-      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:
-      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"
+  - - meta:
+        qualifier: val
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        qualifier: path
+        type: file
+        description: Single input BAM file.
+        pattern: "*.bam"
+    - bai:
+        qualifier: path
+        type: file
+        description: The BAI file for the input BAM file
+        pattern: "*.bai"
+    - read_group_settings:
+        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"
+        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:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+  - data:
+      - meta:
+          qualifier: val
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_mergedReads.bam":
+          type: file
+          description: A BAM file with suffix_mergedReads.bam
+          pattern: "*_mergedReads.bam"
+          qualifier: path
+      - "*.txt.gz":
+          type: file
+          description: A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz
+          pattern: "*.txt.gz"
+          qualifier: path
   - versions:
-      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"
+      - versions.yml:
+          qualifier: path
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 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

@@ -17,55 +17,98 @@ tools:
       documentation: https://bio-bwa.sourceforge.net/bwa.shtml
       arxiv: arXiv:1303.3997
       licence: ["GPL-3.0-or-later"]
+      identifier: "biotools:bwa"
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information.
-        e.g. [ id:'test', single_end:false ]
-  - index:
-      type: file
-      description: BWA genome index files
-      pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
-  - fasta:
-      type: file
-      description: Reference genome in FASTA format
-      pattern: "*.{fasta,fa}"
-  - sort_bam:
-      type: boolean
-      description: use samtools sort (true) or samtools view (false)
-      pattern: "true or false"
+  - - meta:
+        qualifier: val
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - 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:
+        qualifier: val
+        type: map
+        description: |
+          Groovy Map containing reference information.
+          e.g. [ id:'test', single_end:false ]
+    - index:
+        qualifier: path
+        type: file
+        description: BWA genome index files
+        pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
+  - - meta3:
+        qualifier: val
+        type: map
+        description: |
+          Groovy Map containing reference information.
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        qualifier: path
+        type: file
+        description: Reference genome in FASTA format
+        pattern: "*.{fasta,fa}"
+  - - sort_bam:
+        qualifier: val
+        type: boolean
+        description: use samtools sort (true) or samtools view (false)
+        pattern: "true or false"
 output:
   - bam:
-      type: file
-      description: Output BAM file containing read alignments
-      pattern: "*.{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:
-      type: file
-      description: Output CRAM file containing read alignments
-      pattern: "*.{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:
-      type: file
-      description: Optional index file for BAM file
-      pattern: "*.{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:
-      type: file
-      description: Optional index file for CRAM file
-      pattern: "*.{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:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          qualifier: path
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@jeremy1805"