Merge remote-tracking branch 'origin/develop' into somaticSv

CHANGELOG.md

@@ -9,6 +9,15 @@ that users understand how the changes affect the new version.
 -->
 version 5.1.0-dev
 ---------------------------
++ Add optional inputs to macs2, aiming to allow adhering to Encode ATACs-seq. Inputs added:
+  + nomodel
+  + gensz
+  + extsize
+  + shiftsize
+  + pval_thres
+  + bdg
+  + keepdup
+  + callsummits
 + Update samtools image to version 1.16.
 + Add targetsFile input for samtools View.
 + Mateclever's runtime attribute defaults were changed to:

macs2.wdl

@@ -30,6 +30,13 @@ task PeakCalling {
         String sampleName
         String format = "AUTO"
         Boolean nomodel = false
+        String? gensz
+        Int? extsize
+        Int? shiftsize
+        Float? pval_thres
+        Boolean bdg = false
+        String? keepdup
+        Boolean callsummits = false
         Int timeMinutes = 600  # Default to 10 hours
         String memory = "8GiB"
         String dockerImage = "quay.io/biocontainers/macs2:2.1.2--py27r351_0"
@@ -42,8 +49,15 @@ task PeakCalling {
         ~{true="--control" false="" length(controlBams) > 0} ~{sep = ' ' controlBams} \
         --outdir ~{outDir} \
         --name ~{sampleName} \
-        -f ~{format} \
-        ~{true='--nomodel' false='' nomodel}
+        ~{"-f" + format} \
+        ~{"-g" + gensz} \
+        ~{"-p" + pval_thres} \
+        ~{"--shift" + shiftsize} \
+        ~{"--extsize" + extsize} \
+        ~{true='--nomodel' false='' nomodel} \
+        ~{true='-B' false='' bdg} \
+        ~{"--keep-dup" + keepdup} \
+        ~{true='--call-summits' false='' callsummits}
     }
 
     output {
@@ -64,6 +78,13 @@ task PeakCalling {
         sampleName: {description: "Name of the sample to be analysed", category: "required"}
         outDir: {description: "All output files will be written in this directory.", category: "advanced"}
         nomodel: {description: "Whether or not to build the shifting model.", category: "advanced"}
+        gensz: {description: "macs2 argument for setting the mappable genome size or effective genome size which is defined as the genome size which can be sequenced.", category: "advanced"}
+        pval_thres: {description: "macs2 argument for setting the p-value cutoff. If -p is specified, MACS2 will use p-value instead of q-value.", category: "advanced"}
+        shiftsize: {description: "macs2 argument to set an arbitrary shift in bp. Can be negative to indicate direction.", category: "advanced"}
+        extsize: {description: "macs2 argument to extend reads in 5'->3' direction to fix-sized fragments.", category: "advanced"}
+        bdg: {description: "macs2 argument that enables the storage of the fragment pileup, control lambda in bedGraph files.", category: "advanced"}
+        keepdup: {description: "macs2 argument that controls the behavior towards duplicate tags at the exact same location.", category: "advanced"}
+        callsummits: {description: "macs2 argument to reanalyze the shape of signal profile to deconvolve subpeaks within each peak called from the general procedure.", category: "advanced"}
         memory: {description: "The amount of memory this job will use.", 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"}