Merge branch 'develop' into Pacbio-variantcalling

CHANGELOG.md

@@ -16,6 +16,7 @@ version 5.0.0-dev
 + isoseq3: Add required bam index input to isoseq3.
 + pbbam: Add task for indexing PacBio bam files
 + picard: Add CollectHsMetrics and CollectVariantCallingMetrics.
++ Samtools: Add `threads` to parameter meta for Merge task.
 + bcftools: add tmpDir input to specify temporary directory when sorting.
 + bcftools: remove outputType and implement indexing based on output file extension. 
 + NanoPack: Add parameter_meta to NanoPlot task.

samtools.wdl

@@ -362,7 +362,7 @@ task Merge {
         # inputs
         bamFiles: {description: "The BAM files to merge.", category: "required"}
         outputBamPath: {description: "The location the merged BAM file should be written to.", category: "common"}
-        threads: {description: "Number of threads to use.", category: "common"}
+        threads: {description: "Number of threads to use.", category: "advanced"}
         force: {description: "Equivalent to samtools merge's `-f` flag.", 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.",