make samtools/convert follow output guidelines (nf-core#5060)

modules/nf-core/samtools/convert/main.nf

@@ -13,8 +13,11 @@ process SAMTOOLS_CONVERT {
     tuple val(meta3), path(fai)
 
     output:
-    tuple val(meta), path("*.{cram,bam}"), path("*.{crai,bai}") , emit: alignment_index
-    path  "versions.yml"                                        , emit: versions
+    tuple val(meta), path("*.bam")  , emit: bam ,   optional: true
+    tuple val(meta), path("*.cram") , emit: cram,   optional: true
+    tuple val(meta), path("*.bai")  , emit: bai ,   optional: true
+    tuple val(meta), path("*.crai") , emit: crai,   optional: true
+    path  "versions.yml"            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/samtools/convert/meta.yml

@@ -39,10 +39,22 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - alignment_index:
+  - bam:
       type: file
-      description: filtered/converted BAM/CRAM file + index
-      pattern: "*{.bam/cram,.bai/crai}"
+      description: filtered/converted BAM file
+      pattern: "*{.bam}"
+  - cram:
+      type: file
+      description: filtered/converted CRAM file
+      pattern: "*{cram}"
+  - bai:
+      type: file
+      description: filtered/converted BAM index
+      pattern: "*{.bai}"
+  - crai:
+      type: file
+      description: filtered/converted CRAM index
+      pattern: "*{.crai}"
   - version:
       type: file
       description: File containing software version
@@ -53,3 +65,4 @@ authors:
 maintainers:
   - "@FriederikeHanssen"
   - "@maxulysse"
+  - "@matthdsm"

modules/nf-core/samtools/convert/tests/main.nf.test

@@ -34,9 +34,9 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.alignment_index[0][1]).name).match("bam_alignment_index_1") },
-                { assert snapshot(file(process.out.alignment_index[0][2]).name).match("bam_alignment_index_2") },
-                { assert snapshot(process.out.versions).match("bam_versions") }
+                { assert snapshot(file(process.out.cram[0][1]).name).match("bam_to_cram_alignment") },
+                { assert snapshot(file(process.out.crai[0][1]).name).match("bam_to_cram_index") },
+                { assert snapshot(process.out.versions).match("bam_to_cram_versions") }
             )
         }
     }
@@ -66,9 +66,9 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.alignment_index[0][1]).name).match("cram_alignment_index_1") },
-                { assert snapshot(file(process.out.alignment_index[0][2]).name).match("cram_alignment_index_2") },
-                { assert snapshot(process.out.versions).match("cram_versions") }
+                { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_alignment") },
+                { assert snapshot(file(process.out.bai[0][1]).name).match("cram_to_bam_alignment_index") },
+                { assert snapshot(process.out.versions).match("cram_to_bam_versions") }
             )
         }
     }