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

@@ -1,46 +1,51 @@
 name: picard_markduplicates
 description: Locate and tag duplicate reads in a BAM file
 keywords:
-    - markduplicates
-    - pcr
-    - duplicates
-    - bam
-    - sam
-    - cram
+  - markduplicates
+  - pcr
+  - duplicates
+  - bam
+  - sam
+  - cram
 tools:
-    - picard:
-        description: |
-            A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
-            data and formats such as SAM/BAM/CRAM and VCF.
-        homepage: https://broadinstitute.github.io/picard/
-        documentation: https://broadinstitute.github.io/picard/
+  - picard:
+      description: |
+        A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+        data and formats such as SAM/BAM/CRAM and VCF.
+      homepage: https://broadinstitute.github.io/picard/
+      documentation: https://broadinstitute.github.io/picard/
 input:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - bam:
-        type: file
-        description: BAM file
-        pattern: "*.{bam}"
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.{bam}"
 output:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - bam:
-        type: file
-        description: BAM file with duplicate reads marked/removed
-        pattern: "*.{bam}"
-    - metrics:
-        type: file
-        description: Duplicate metrics file generated by picard
-        pattern: "*.{metrics.txt}"
-    - version:
-        type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      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
+      pattern: "*.{metrics.txt}"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
 authors:
-    - "@drpatelh"
+  - "@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: