update picard/collecthsmetrics (#1542)

* update picard/collecthsmetrics

* syntax fixes, bugfixes

* add tests

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

modules/picard/collecthsmetrics/main.nf

@@ -15,8 +15,8 @@ process PICARD_COLLECTHSMETRICS {
     path target_intervals
 
     output:
-    tuple val(meta), path("*collecthsmetrics.txt"), emit: hs_metrics
-    path "versions.yml"                           , emit: versions
+    tuple val(meta), path("*_metrics")  , emit: metrics
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -41,7 +41,8 @@ process PICARD_COLLECTHSMETRICS {
         -BAIT_INTERVALS $bait_intervals \\
         -TARGET_INTERVALS $target_intervals \\
         -INPUT $bam \\
-        -OUTPUT ${prefix}_collecthsmetrics.txt
+        -OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
+
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -52,7 +53,7 @@ process PICARD_COLLECTHSMETRICS {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}_collecthsmetrics.txt
+    touch ${prefix}.CollectHsMetrics.coverage_metrics
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/picard/collecthsmetrics/meta.yml

@@ -57,10 +57,11 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - hs_metrics:
+  - metrics:
       type: file
-      description: The metrics file.
-      pattern: "*_collecthsmetrics.txt"
+      description: Alignment metrics files generated by picard
+      pattern: "*_{metrics}"
 
 authors:
   - "@projectoriented"
+  - "@matthdsm"

tests/modules/picard/collecthsmetrics/main.nf

@@ -7,7 +7,7 @@ include { PICARD_COLLECTHSMETRICS } from '../../../../modules/picard/collecthsme
 workflow test_picard_collecthsmetrics {
 
     input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
 
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)

tests/modules/picard/collecthsmetrics/test.yml

@@ -5,4 +5,4 @@
     - picard/collecthsmetrics
   files:
     # The file can't be md5'd consistently
-    - path: output/picard/test_collecthsmetrics.txt
+    - path: output/picard/test.CollectHsMetrics.coverage_metrics