Merge branch 'master' into fix-ci-confirm-pass

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

@@ -6,29 +6,44 @@ process SAMTOOLS_MPILEUP {
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
         'biocontainers/samtools:1.21--h50ea8bc_0' }"
+
     input:
     tuple val(meta), path(input), path(intervals)
     path  fasta
 
     output:
     tuple val(meta), path("*.mpileup.gz"), emit: mpileup
-    path  "versions.yml"                           , emit: versions
+    path  "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    intervals = intervals ? "-l ${intervals}" : ""
+    def intervals_arg = intervals ? "-l ${intervals}" : ""
     """
     samtools mpileup \\
         --fasta-ref $fasta \\
         --output ${prefix}.mpileup \\
         $args \\
-        $intervals \\
+        $intervals_arg \\
         $input
     bgzip ${prefix}.mpileup
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def intervals_arg = intervals ? "-l ${intervals}" : ""
+    """
+    touch ${prefix}.mpileup.gz
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')