Merge pull request #275 from biowdl/refOptional

Make referenceAnnotation optional in GffCompare and add minimumCoverage for stringtie

CHANGELOG.md

@@ -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

gffcompare.wdl

@@ -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} \

htseq.wdl

@@ -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"
     }
 

stringtie.wdl

@@ -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"}