update args & convert to bam (#1355)

modules/picard/cleansam/main.nf

@@ -1,6 +1,6 @@
 process PICARD_CLEANSAM {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -8,10 +8,10 @@ process PICARD_CLEANSAM {
         'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(sam)
+    tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("*.sam"), emit: sam
+    tuple val(meta), path("*.bam"), emit: bam
     path "versions.yml"           , emit: versions
 
     when:
@@ -20,7 +20,6 @@ process PICARD_CLEANSAM {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def STRINGENCY = task.ext.stringency ?: "STRICT"
     def avail_mem = 3
     if (!task.memory) {
         log.info '[Picard CleanSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -32,9 +31,8 @@ process PICARD_CLEANSAM {
         -Xmx${avail_mem}g \\
         CleanSam  \\
         ${args} \\
-        -I ${sam} \\
+        -I ${bam} \\
-        -O ${prefix}.sam \\
+        -O ${prefix}.bam
-        --VALIDATION_STRINGENCY ${STRINGENCY}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/picard/cleansam/meta.yml

@@ -1,8 +1,7 @@
 name: picard_cleansam
-description: Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
+description: Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
 keywords:
   - clean
-  - sam
   - bam
 tools:
   - picard:
@@ -22,8 +21,8 @@ input:
         e.g. [ id:'test', single_end:false ]
   - sam:
       type: file
-      description: SAM file
+      description: BAM file
-      pattern: "*.{sam}"
+      pattern: "*.{bam}"
 
 output:
   - meta:
@@ -37,8 +36,8 @@ output:
       pattern: "versions.yml"
   - sam:
       type: file
-      description: Cleaned SAM file
+      description: Cleaned BAM file
-      pattern: "*.{sam}"
+      pattern: "*.{bam}"
 
 authors:
   - "@sateeshperi"

tests/modules/picard/cleansam/test.yml

@@ -4,7 +4,7 @@
     - picard/cleansam
     - picard
   files:
-    - path: output/picard/test.sam
+    - path: output/picard/test.bam
-      md5sum: e314171a6060eb79947c13ad126ddf00
+      md5sum: a48f8e77a1480445efc57570c3a38a68
     - path: output/picard/versions.yml
       md5sum: e6457d7c6de51bf6f4b577eda65e57ac