Update to topics braker3

modules/nf-core/braker3/main.nf

@@ -23,7 +23,10 @@ process BRAKER3 {
     tuple val(meta), path("$prefix/hintsfile.gff")      , emit: hintsfile   , optional: true
     tuple val(meta), path("$prefix/braker.gff3")        , emit: gff3        , optional: true
     tuple val(meta), path("$prefix/what-to-cite.txt")   , emit: citations
-    path "versions.yml"                                 , emit: versions
+    tuple val("${task.process}"), val('braker3'), eval("braker.pl --version 2>/dev/null | sed 's/braker.pl version //'"), emit: versions_braker3, topic: versions
+    tuple val("${task.process}"), val('augustus'), eval("augustus --version |& sed -n 's/AUGUSTUS (\\(.*\\)) is a gene .*/\\1/p'"), emit: versions_augustus, topic: versions
+    tuple val("${task.process}"), val('genemark-etp'), eval("gmetp.pl |& sed -n 's/ETP version \\(.*\\)/\\1/p'"), emit: versions_genemarketp, topic: versions
+    tuple val("${task.process}"), val('prothint'), eval("prothint.py --version |& sed 's/prothint.py //1'"), emit: versions_prothint, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -60,14 +63,6 @@ process BRAKER3 {
         $prot_arg \\
         $hints \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        braker3: \$(braker.pl --version 2>/dev/null | sed 's/braker.pl version //')
-        augustus: \$(augustus --version |& sed -n 's/AUGUSTUS (\\(.*\\)) is a gene .*/\\1/p')
-        genemark-etp: \$(echo "\$(gmetp.pl || echo '')" | sed -n 's/ETP version \\(.*\\)/\\1/p')
-        prothint: \$(prothint.py --version | sed 's/prothint.py //1')
-    END_VERSIONS
     """
 
     stub:
@@ -87,13 +82,5 @@ process BRAKER3 {
     touch "$prefix/braker.log"
     touch "$prefix/what-to-cite.txt"
     $touch_gff
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        braker3: \$(braker.pl --version 2>/dev/null | sed 's/braker.pl version //')
-        augustus: \$(augustus --version |& sed -n 's/AUGUSTUS (\\(.*\\)) is a gene .*/\\1/p')
-        genemark-etp: \$(echo "\$(gmetp.pl || echo '')" | sed -n 's/ETP version \\(.*\\)/\\1/p')
-        prothint: \$(prothint.py --version | sed 's/prothint.py //1')
-    END_VERSIONS
     """
 }

modules/nf-core/braker3/meta.yml

@@ -15,9 +15,9 @@ tools:
       documentation: https://github.com/Gaius-Augustus/BRAKER
       tool_dev_url: https://github.com/Gaius-Augustus/BRAKER
       doi: "10.13140/RG.2.2.20047.36004"
-      licence: ["Artistic-1.0"]
+      licence:
+        - "Artistic-1.0"
       identifier: biotools:braker3
-
 input:
   - - meta:
         type: map
@@ -28,93 +28,187 @@ input:
         type: file
         description: Genome assembly fasta
         pattern: "*.{fasta,fa,fas,faa,fna}"
-  - - bam:
-        type: file
-        description: BAM file of RNA-seq data to be passed to --bam
-        pattern: "*.bam"
-  - - rnaseq_sets_dirs:
-        type: file
-        description: Directories of RNA-seq data sets to be passed to --rnaseq_sets_dirs
-  - - rnaseq_sets_ids:
-        type: file
-        description: IDs of RNA-seq data sets to be passed to --rnaseq_sets_ids
-  - - proteins:
-        type: file
-        description: Protein evidence to be passed to --proteins
-        pattern: "*.{fasta,fa,fas,faa}"
-  - - hintsfile:
-        type: file
-        description: Hintsfile to be passed to --hintsfile
-        pattern: "*.{gff, gtf, gff3}"
+        ontologies: []
+  - bam:
+      type: file
+      description: BAM file of RNA-seq data to be passed to --bam
+      pattern: "*.bam"
+      ontologies: []
+  - rnaseq_sets_dirs:
+      type: file
+      description: Directories of RNA-seq data sets to be passed to
+        --rnaseq_sets_dirs
+      ontologies: []
+  - rnaseq_sets_ids:
+      type: file
+      description: IDs of RNA-seq data sets to be passed to --rnaseq_sets_ids
+      ontologies: []
+  - proteins:
+      type: file
+      description: Protein evidence to be passed to --proteins
+      pattern: "*.{fasta,fa,fas,faa}"
+      ontologies: []
+  - hintsfile:
+      type: file
+      description: Hintsfile to be passed to --hintsfile
+      pattern: "*.{gff, gtf, gff3}"
+      ontologies: []
 output:
   gtf:
     - - meta:
           type: file
           description: Gene transfer format file as output by BRAKER3
           pattern: "*.{gtf}"
-    - $prefix/braker.gtf:
-        type: file
-        description: Gene transfer format file as output by BRAKER3
-        pattern: "*.{gtf}"
+          ontologies: []
+      - $prefix/braker.gtf:
+          type: file
+          description: Gene transfer format file as output by BRAKER3
+          pattern: "*.{gtf}"
+          ontologies: []
   cds:
     - - meta:
+          type: file
+          description: Gene transfer format file as output by BRAKER3
+          pattern: "*.{gtf}"
+          ontologies: []
+      - $prefix/braker.codingseq:
           type: file
           description: Coding sequence file as output by BRAKER3
           pattern: "*.{codingseq}"
-    - $prefix/braker.codingseq:
-        type: file
-        description: Coding sequence file as output by BRAKER3
-        pattern: "*.{codingseq}"
+          ontologies: []
   aa:
     - - meta:
+          type: file
+          description: Gene transfer format file as output by BRAKER3
+          pattern: "*.{gtf}"
+          ontologies: []
+      - $prefix/braker.aa:
           type: file
           description: Protein sequence file as output by BRAKER3
           pattern: "*.{aa}"
-    - $prefix/braker.aa:
-        type: file
-        description: Protein sequence file as output by BRAKER3
-        pattern: "*.{aa}"
+          ontologies: []
   log:
     - - meta:
+          type: file
+          description: Gene transfer format file as output by BRAKER3
+          pattern: "*.{gtf}"
+          ontologies: []
+      - $prefix/braker.log:
           type: file
           description: BRAKER3 log file
           pattern: "*.log"
-    - $prefix/braker.log:
-        type: file
-        description: BRAKER3 log file
-        pattern: "*.log"
+          ontologies: []
   hintsfile:
     - - meta:
+          type: file
+          description: Gene transfer format file as output by BRAKER3
+          pattern: "*.{gtf}"
+          ontologies: []
+      - $prefix/hintsfile.gff:
           type: file
           description: Hints file as output by BRAKER3
           pattern: "*hintsfile.{gff}"
-    - $prefix/hintsfile.gff:
-        type: file
-        description: Hints file as output by BRAKER3
-        pattern: "*hintsfile.{gff}"
+          ontologies: []
   gff3:
     - - meta:
+          type: file
+          description: Gene transfer format file as output by BRAKER3
+          pattern: "*.{gtf}"
+          ontologies: []
+      - $prefix/braker.gff3:
           type: file
           description: GFF3 file as output by BRAKER3
           pattern: "*.{gff3}"
-    - $prefix/braker.gff3:
-        type: file
-        description: GFF3 file as output by BRAKER3
-        pattern: "*.{gff3}"
+          ontologies: []
   citations:
     - - meta:
+          type: file
+          description: Gene transfer format file as output by BRAKER3
+          pattern: "*.{gtf}"
+          ontologies: []
+      - $prefix/what-to-cite.txt:
           type: file
           description: BRAKER3 citations
           pattern: "what-to-cite.txt"
-    - "$prefix/what-to-cite.txt":
-        type: file
-        description: BRAKER3 citations
-        pattern: "what-to-cite.txt"
+          ontologies: []
+  versions_braker3:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - braker3:
+          type: string
+          description: The name of the tool
+      - braker.pl --version 2>/dev/null | sed 's/braker.pl version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_augustus:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - augustus:
+          type: string
+          description: The name of the tool
+      - augustus --version |& sed -n 's/AUGUSTUS (\(.*\)) is a gene .*/\1/p':
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_genemarketp:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - genemark-etp:
+          type: string
+          description: The name of the tool
+      - gmetp.pl |& sed -n 's/ETP version \(.*\)/\1/p':
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_prothint:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - prothint:
+          type: string
+          description: The name of the tool
+      - prothint.py --version |& sed 's/prothint.py //1':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - braker3:
+          type: string
+          description: The name of the tool
+      - braker.pl --version 2>/dev/null | sed 's/braker.pl version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - augustus:
+          type: string
+          description: The name of the tool
+      - augustus --version |& sed -n 's/AUGUSTUS (\(.*\)) is a gene .*/\1/p':
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - genemark-etp:
+          type: string
+          description: The name of the tool
+      - gmetp.pl |& sed -n 's/ETP version \(.*\)/\1/p':
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - prothint:
+          type: string
+          description: The name of the tool
+      - prothint.py --version |& sed 's/prothint.py //1':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@kherronism"
   - "@GallVp"

modules/nf-core/braker3/tests/main.nf.test

@@ -15,7 +15,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test' ], // meta map
+                    [ id:'test' ],
                     file('https://raw.githubusercontent.com/Gaius-Augustus/BRAKER/f58479fe5bb13a9e51c3ca09cb9e137cab3b8471/example/genome.fa', checkIfExists: true)
                 ]
                 input[1] = file('http://topaz.gatech.edu/GeneMark/Braker/RNAseq.bam', checkIfExists: true)
@@ -30,16 +30,16 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert file(process.out.log[0][1]).text.contains('BRAKER RUN FINISHED') },
                 { assert snapshot(
                     process.out.aa,
                     process.out.cds,
                     process.out.citations,
                     process.out.gff3,
                     process.out.gtf,
                     process.out.hintsfile,
-                    process.out.versions,
-                    ).match() },
-                { assert file(process.out.log[0][1]).text.contains('BRAKER RUN FINISHED') }
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
             )
         }
 
@@ -53,7 +53,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test' ], // meta map
+                    [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
                 ]
                 input[1] = []
@@ -68,7 +68,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }