modify markduplicates module (#681)

* tested

* updated meta config and test config

modules/picard/markduplicates/main.nf

@@ -23,6 +23,7 @@ process PICARD_MARKDUPLICATES {
 
     output:
     tuple val(meta), path("*.bam")        , emit: bam
+    tuple val(meta), path("*.bai")        , optional:true, emit: bai
     tuple val(meta), path("*.metrics.txt"), emit: metrics
     path  "*.version.txt"                 , emit: version
 
@@ -40,9 +41,9 @@ process PICARD_MARKDUPLICATES {
         -Xmx${avail_mem}g \\
         MarkDuplicates \\
         $options.args \\
-        INPUT=$bam \\
-        OUTPUT=${prefix}.bam \\
-        METRICS_FILE=${prefix}.MarkDuplicates.metrics.txt
+        -I $bam \\
+        -O ${prefix}.bam \\
+        -M ${prefix}.MarkDuplicates.metrics.txt
 
     echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt
     """

modules/picard/markduplicates/meta.yml

@@ -34,6 +34,10 @@ output:
       type: file
       description: BAM file with duplicate reads marked/removed
       pattern: "*.{bam}"
+  - bai:
+      type: file
+      description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag
+      pattern: "*.{bai}"
   - metrics:
       type: file
       description: Duplicate metrics file generated by picard
@@ -44,3 +48,4 @@ output:
       pattern: "*.{version.txt}"
 authors:
   - "@drpatelh"
+  - "@projectoriented"

tests/modules/picard/markduplicates/test.yml

@@ -6,8 +6,7 @@
   files:
     - path: ./output/picard/test.MarkDuplicates.metrics.txt
     - path: ./output/picard/test.bam
-      md5sum: 3270bb142039e86aaf2ab83c540225d5
-
+      md5sum: b520ccdc3a9edf3c6a314983752881f2
 - name: picard markduplicates on unsorted bam
   command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
   tags: