Unverified Commit 1a46ce88 authored by Cats's avatar Cats Committed by GitHub
Browse files

Merge pull request #275 from biowdl/refOptional

Make referenceAnnotation optional in GffCompare and add minimumCoverage for stringtie
parents cdbcd68d 8ed8a020
......@@ -10,6 +10,8 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
+ GffCompare: Make the `referenceAnnotation` input optional.
+ Stringtie: Add the `minimumCoverage` input.
+ UMI-tools: update default dockerImage to use umitools v1.1.1 with correct samtools version (1.10)
+ UMI-tools: re-introduce samtools indexing
+ UMI-tools: update default dockerImage to use umitools v1.1.1
......
......@@ -23,7 +23,6 @@ version 1.0
task GffCompare {
input {
Array[File] inputGtfFiles
File referenceAnnotation
# gffcmp is the default used by the program as well. This needs to be
# defined in order for the output values to be consistent and correct.
String outPrefix = "gffcmp"
......@@ -40,6 +39,7 @@ task GffCompare {
Boolean debugMode = false
File? inputGtfList
File? referenceAnnotation
String? outputDir
File? genomeSequences
Int? maxDistanceFreeEndsTerminalExons
......@@ -64,7 +64,7 @@ task GffCompare {
set -e
~{"mkdir -p " + outputDir}
gffcompare \
-r ~{referenceAnnotation} \
~{"-r " + referenceAnnotation} \
~{"-o '" + totalPrefix + "'"} \
~{"-s " + genomeSequences} \
~{"-e " + maxDistanceFreeEndsTerminalExons} \
......
......@@ -34,7 +34,7 @@ task HTSeqCount {
Int nprocesses = 1
String memory = "8G"
Int timeMinutes = 10 + ceil(size(inputBams, "G") * 60)
Int timeMinutes = 1440 #10 + ceil(size(inputBams, "G") * 60) FIXME
String dockerImage = "quay.io/biocontainers/htseq:0.12.4--py37hb3f55d8_0"
}
......
......@@ -31,6 +31,7 @@ task Stringtie {
Boolean? firstStranded
Boolean? secondStranded
String? geneAbundanceFile
Float? minimumCoverage
Int threads = 1
String memory = "2G"
......@@ -47,6 +48,7 @@ task Stringtie {
~{true="-e" false="" skipNovelTranscripts} \
~{true="--rf" false="" firstStranded} \
~{true="--fr" false="" secondStranded} \
~{"-c " + minimumCoverage} \
-o ~{assembledTranscriptsFile} \
~{"-A " + geneAbundanceFile} \
~{bam}
......@@ -74,6 +76,7 @@ task Stringtie {
firstStranded: {description: "Equivalent to the --rf flag of stringtie.", category: "required"}
secondStranded: {description: "Equivalent to the --fr flag of stringtie.", category: "required"}
geneAbundanceFile: {description: "Where the abundance file should be written.", category: "common"}
minimumCoverage: {description: "The minimum coverage for a transcript to be shown in the output.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory needed for this task in GB.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment