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Commit c85f016a authored by Cats's avatar Cats
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Merge remote-tracking branch 'origin/develop' into somaticSv

parents 2b4fb7ea 24f6a069
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......@@ -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:
......
......@@ -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"}
......
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