Swap bwa/mem to topic and combine output channels

modules/nf-core/bwa/mem/main.nf

@@ -14,11 +14,10 @@ process BWA_MEM {
     val   sort_bam
 
     output:
-    tuple val(meta), path("*.bam")  , emit: bam,    optional: true
-    tuple val(meta), path("*.cram") , emit: cram,   optional: true
-    tuple val(meta), path("*.csi")  , emit: csi,    optional: true
-    tuple val(meta), path("*.crai") , emit: crai,   optional: true
-    path  "versions.yml"            , emit: versions
+    tuple val(meta), path("*.{sam,bam,cram}"), emit: output
+    tuple val(meta), path("*.{csi,bai,crai}"), emit: index , optional: true
+    tuple val("${task.process}"), val('bwa'), eval('bwa 2>&1 | sed -n "s/^Version: //p"'), topic: versions, emit: versions_bwa
+    tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools
 
     when:
     task.ext.when == null || task.ext.when
@@ -43,13 +42,11 @@ process BWA_MEM {
         -t $task.cpus \\
         \$INDEX \\
         $reads \\
-        | samtools $samtools_command $args2 ${reference} --threads $task.cpus -o ${prefix}.${extension} -
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
+        | samtools $samtools_command \\
+        $args2 \\
+        ${reference} \\
+        --threads $task.cpus \\
+        -o ${prefix}.${extension} -
     """
 
     stub:
@@ -60,15 +57,10 @@ process BWA_MEM {
                     sort_bam && args2.contains("-O cram")? "cram":
                     !sort_bam && args2.contains("-C")    ? "cram":
                     "bam"
+    def index_cmd = extension == "bam"  ? "touch ${prefix}.csi" :
+                     extension == "cram" ? "touch ${prefix}.crai" : ""
     """
     touch ${prefix}.${extension}
-    touch ${prefix}.csi
-    touch ${prefix}.crai
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
+    ${index_cmd}
     """
 }

modules/nf-core/bwa/mem/meta.yml

@@ -60,57 +60,71 @@ input:
       description: use samtools sort (true) or samtools view (false)
       pattern: "true or false"
 output:
-  bam:
+  output:
     - - meta:
           type: map
           description: Groovy Map containing sample information
-      - "*.bam":
+      - "*.{sam,bam,cram}":
           type: file
-          description: Output BAM file containing read alignments
-          pattern: "*.{bam}"
+          description: Output SAM/BAM/CRAM file containing read alignments
+          pattern: "*.{sam,bam,cram}"
           ontologies:
             - edam: "http://edamontology.org/format_2572" # BAM
-  cram:
-    - - meta:
-          type: file
-          description: Output BAM file containing read alignments
-          ontologies: []
-      - "*.cram":
-          type: file
-          description: Output CRAM file containing read alignments
-          pattern: "*.{cram}"
-          ontologies:
             - edam: "http://edamontology.org/format_3462" # CRAM
-  csi:
+  index:
     - - meta:
           type: map
           description: Groovy Map containing sample information
-      - "*.csi":
+      - "*.{csi,bai,crai}":
           type: file
-          description: Optional index file for BAM file
-          pattern: "*.{csi}"
-          ontologies: []
-  crai:
-    - - meta:
-          type: map
-          description: Groovy Map containing sample information
-      - "*.crai":
-          type: file
-          description: Optional index file for CRAM file
-          pattern: "*.{crai}"
+          description: Optional index file for BAM/CRAM file
+          pattern: "*.{csi,bai,crai}"
           ontologies: []
+  versions_bwa:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - bwa:
+          type: string
+          description: The tool name
+      - 'bwa 2>&1 | sed -n "s/^Version: //p"':
+          type: string
+          description: The command used to generate the version of the tool
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - samtools:
+          type: string
+          description: The tool name
+      - "samtools version | sed '1!d;s/.* //'":
+          type: string
+          description: The command used to generate the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - bwa:
+          type: string
+          description: The tool name
+      - 'bwa 2>&1 | sed -n "s/^Version: //p"':
+          type: string
+          description: The command used to generate the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - samtools:
+          type: string
+          description: The tool name
+      - "samtools version | sed '1!d;s/.* //'":
+          type: string
+          description: The command used to generate the version of the tool
+
 authors:
   - "@drpatelh"
   - "@jeremy1805"
   - "@matthdsm"
 maintainers:
-  - "@drpatelh"
   - "@jeremy1805"
   - "@matthdsm"

modules/nf-core/bwa/mem/tests/main.nf.test

@@ -45,11 +45,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.cram,
-                    process.out.csi,
-                    process.out.crai,
-                    process.out.versions,
-                    bam(process.out.bam[0][1]).getReadsMD5()
+                    process.out.index,
+                    process.out.findAll { key, val -> key.startsWith("versions") },
+                    bam(process.out.output[0][1]).getReadsMD5()
                     ).match()
                 }
             )
@@ -79,10 +77,8 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.cram,
-                    process.out.csi,
-                    process.out.crai,
-                    process.out.versions,
+                    process.out.index,
+                    process.out.findAll { key, val -> key.startsWith("versions") },
                     bam(process.out.bam[0][1]).getReadsMD5()
                     ).match()
                 }
@@ -114,11 +110,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.cram,
-                    process.out.csi,
-                    process.out.crai,
-                    process.out.versions,
-                    bam(process.out.bam[0][1]).getReadsMD5()
+                    process.out.index,
+                    process.out.findAll { key, val -> key.startsWith("versions") },
+                    bam(process.out.output[0][1]).getReadsMD5()
                     ).match()
                 }
             )
@@ -149,11 +143,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.cram,
-                    process.out.csi,
-                    process.out.crai,
-                    process.out.versions,
-                    bam(process.out.bam[0][1]).getReadsMD5()
+                    process.out.index,
+                    process.out.findAll { key, val -> key.startsWith("versions") },
+                    bam(process.out.output[0][1]).getReadsMD5()
                     ).match()
                 }
             )
@@ -184,11 +176,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.cram,
-                    process.out.csi,
-                    process.out.crai,
-                    process.out.versions,
-                    bam(process.out.bam[0][1]).getReadsMD5()
+                    process.out.index,
+                    process.out.findAll { key, val -> key.startsWith("versions") },
+                    bam(process.out.output[0][1]).getReadsMD5()
                     ).match()
                 }
             )