Bulk update meta yml modules

modules/nf-core/abacas/meta.yml

@@ -14,40 +14,43 @@ tools:
       documentation: http://abacas.sourceforge.net/documentation.html
       doi: "10.1093/bioinformatics/btp347"
       licence: ["GPL v2-or-later"]
+      identifier: biotools:abacas
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - scaffold:
-      type: file
-      description: Fasta file containing scaffold
-      pattern: "*.{fasta,fa}"
-  - fasta:
-      type: file
-      description: FASTA reference file
-      pattern: "*.{fasta,fa}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - scaffold:
+        type: file
+        description: Fasta file containing scaffold
+        pattern: "*.{fasta,fa}"
+  - - fasta:
+        type: file
+        description: FASTA reference file
+        pattern: "*.{fasta,fa}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - results:
-      type: file
-      description: |
-        List containing abacas output files
-        [ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps',
-        'test.abacas.gaps.tab', 'test.abacas.nucmer.delta',
-        'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling',
-        'test.abacas.tab', 'test.abacas.unused.contigs.out',
-        'test.abacas.MULTIFASTA.fa' ]
-      pattern: "*.{abacas}*"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.abacas*":
+          type: file
+          description: |
+            List containing abacas output files
+            [ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps',
+            'test.abacas.gaps.tab', 'test.abacas.nucmer.delta',
+            'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling',
+            'test.abacas.tab', 'test.abacas.unused.contigs.out',
+            'test.abacas.MULTIFASTA.fa' ]
+          pattern: "*.{abacas}*"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@joseespinosa"
   - "@drpatelh"

modules/nf-core/abricate/run/meta.yml

@@ -11,34 +11,38 @@ tools:
       documentation: https://github.com/tseemann/abricate
       tool_dev_url: https://github.com/tseemann/abricate
       licence: ["GPL v2"]
+      identifier: biotools:ABRicate
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - assembly:
-      type: file
-      description: FASTA, GenBank or EMBL formatted file
-      pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
-  - databasedir:
-      type: directory
-      description: Optional location of local copy of database files, possibly with custom databases set up with `abricate --setupdb`
-      pattern: "*/"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - assembly:
+        type: file
+        description: FASTA, GenBank or EMBL formatted file
+        pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
+  - - databasedir:
+        type: directory
+        description: Optional location of local copy of database files, possibly with
+          custom databases set up with `abricate --setupdb`
+        pattern: "*/"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - report:
-      type: file
-      description: Tab-delimited report of results
-      pattern: "*.{txt}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.txt":
+          type: file
+          description: Tab-delimited report of results
+          pattern: "*.{txt}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@rpetit3"
 maintainers:

modules/nf-core/abricate/summary/meta.yml

@@ -11,30 +11,33 @@ tools:
       documentation: https://github.com/tseemann/abricate
       tool_dev_url: https://github.com/tseemann/abricate
       licence: ["GPL v2"]
+      identifier: biotools:ABRicate
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reports:
-      type: file
-      description: FASTA, GenBank or EMBL formatted file
-      pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reports:
+        type: file
+        description: FASTA, GenBank or EMBL formatted file
+        pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - report:
-      type: file
-      description: Tab-delimited report of aggregated results
-      pattern: "*.{txt}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.txt":
+          type: file
+          description: Tab-delimited report of aggregated results
+          pattern: "*.{txt}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@rpetit3"
 maintainers:

modules/nf-core/abritamr/run/meta.yml

@@ -1,54 +1,88 @@
----
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "abritamr_run"
-description: A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes
+description: A NATA accredited tool for reporting the presence of antimicrobial resistance
+  genes in bacterial genomes
 keywords:
   - bacteria
   - fasta
   - antibiotic resistance
 tools:
   - "abritamr":
-      description: "A pipeline for running AMRfinderPlus and collating results into functional classes"
+      description: "A pipeline for running AMRfinderPlus and collating results into
+        functional classes"
       homepage: "https://github.com/MDU-PHL/abritamr"
       documentation: "https://github.com/MDU-PHL/abritamr"
       tool_dev_url: "https://github.com/MDU-PHL/abritamr"
       doi: "10.1038/s41467-022-35713-4"
       licence: ["GPL v3"]
+      identifier: biotools:abritamr
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'test', single_end:false ]`
-  - fasta:
-      type: file
-      description: Assembled contigs in FASTA format
-      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - fasta:
+        type: file
+        description: Assembled contigs in FASTA format
+        pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
 output:
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - matches:
-      type: file
-      description: Tab-delimited file, with a row per sequence, and columns representing functional drug classes
-      pattern: "*.summary_matches.txt"
+      - meta:
+          type: file
+          description: Tab-delimited file, with a row per sequence, and columns representing
+            functional drug classes
+          pattern: "*.summary_matches.txt"
+      - ${prefix}.summary_matches.txt:
+          type: file
+          description: Tab-delimited file, with a row per sequence, and columns representing
+            functional drug classes
+          pattern: "*.summary_matches.txt"
   - partials:
-      type: file
-      description: Tab-delimited file, with a row per sequence, and columns representing partial hits to functional drug classes
-      pattern: "*.summary_partials.txt"
+      - meta:
+          type: file
+          description: Tab-delimited file, with a row per sequence, and columns representing
+            partial hits to functional drug classes
+          pattern: "*.summary_partials.txt"
+      - ${prefix}.summary_partials.txt:
+          type: file
+          description: Tab-delimited file, with a row per sequence, and columns representing
+            partial hits to functional drug classes
+          pattern: "*.summary_partials.txt"
   - virulence:
-      type: string
-      description: Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification
-      pattern: "*.summary_virulence.txt"
-  - txt:
-      type: string
-      description: Tab-delimited file, combining non-empty summary files
-      pattern: "*.abritamr.txt"
+      - meta:
+          type: string
+          description: Tab-delimited file, with a row per sequence, and columns representing
+            AMRFinderPlus virulence gene classification
+          pattern: "*.summary_virulence.txt"
+      - ${prefix}.summary_virulence.txt:
+          type: string
+          description: Tab-delimited file, with a row per sequence, and columns representing
+            AMRFinderPlus virulence gene classification
+          pattern: "*.summary_virulence.txt"
   - out:
-      type: string
-      description: raw output from AMRFinder plus (per sequence)
-      pattern: "*.amrfinder.txt"
+      - meta:
+          type: string
+          description: raw output from AMRFinder plus (per sequence)
+          pattern: "*.amrfinder.txt"
+      - ${prefix}.amrfinder.out:
+          type: string
+          description: raw output from AMRFinder plus (per sequence)
+          pattern: "*.amrfinder.txt"
+  - txt:
+      - meta:
+          type: string
+          description: Tab-delimited file, combining non-empty summary files
+          pattern: "*.abritamr.txt"
+      - ${prefix}.abritamr.txt:
+          type: string
+          description: Tab-delimited file, combining non-empty summary files
+          pattern: "*.abritamr.txt"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@rpetit3"
 maintainers: