add stub for picard/collectwgsmtrics (#1945)

* add stub for picard/collectwgsmtrics

* fix conda build needs to be >2.0 error and typo

modules/picard/collectwgsmetrics/main.nf

@@ -2,7 +2,7 @@ process PICARD_COLLECTWGSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4 r::r-base" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
         'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
@@ -37,6 +37,17 @@ process PICARD_COLLECTWGSMETRICS {
         --REFERENCE_SEQUENCE ${fasta}
 
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.CollectWgsMetrics.coverage_metrics
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)

tests/modules/picard/collectwgsmetrics/test.yml

@@ -5,3 +5,11 @@
     - picard
   files:
     - path: output/picard/test.CollectWgsMetrics.coverage_metrics
+
+- name: picard collectwgsmetrics test_picard_collectwgsmetrics stub
+  command: nextflow run ./tests/modules/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectwgsmetrics/nextflow.config -stub-run
+  tags:
+    - picard/collectwgsmetrics
+    - picard
+  files:
+    - path: output/picard/test.CollectWgsMetrics.coverage_metrics