Add pbmm2 outputPrefix parameter

Author: rhpvorderman

CHANGELOG.md

@@ -10,6 +10,8 @@ that users understand how the changes affect the new version.
 
 version 6.0.0-dev
 ---------------------------
++ Allow pbmm2 to work with a set output prefix for the BAM file.
++ Update pbmm2 docker container to version 1.17
 + Add VEP task.
 + Add Sequali task.
 + Add Clair3 task.

pbmm2.wdl

@@ -25,6 +25,7 @@ task Mapping {
         String presetOption
         Boolean sort=true
         String sample
+        String outputPrefix = sample + ".align"
         File referenceMMI
         File queryFile
 
@@ -35,19 +36,21 @@ task Mapping {
     }
 
     command {
+        set -e 
+        mkdir -p ~{outputPrefix} 
         pbmm2 align \
         --preset ~{presetOption} \
         ~{true="--sort" false="" sort} \
         -j ~{cores} \
         ~{referenceMMI} \
         ~{queryFile} \
         --sample ~{sample} \
-        ~{sample}.align.bam
+        ~{outputPrefix}.bam
     }
 
     output {
-        File outputAlignmentFile = sample + ".align.bam"
-        File outputIndexFile = sample + ".align.bam.bai"
+        File outputAlignmentFile = outputPrefix + ".bam"
+        File outputIndexFile = outputPrefix + ".bam.bai"
     }
 
     runtime {
@@ -62,14 +65,15 @@ task Mapping {
         presetOption: {description: "This option applies multiple options at the same time.", category: "required"}
         sort: {description: "Sort the output bam file.", category: "advanced"}
         sample: {description: "Name of the sample.", category: "required"}
+        outputPrefix: {description: "The prefix of the output filename before the .bam extension." category: "advanced"}
         referenceMMI: {description: "MMI file for the reference.", category: "required"}
         queryFile: {description: "BAM file with reads to align against the reference.", category: "required"}
         cores: {description: "The number of cores to be used.", category: "advanced"}
         memory: {description: "The amount of memory available to the job.", category: "advanced"}
         timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
         dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
 
-        # outputs
+        # output
         outputAlignmentFile: {description: "Mapped bam file."}
         outputIndexFile: {description: "Bam index file."}
     }