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Commit b4fe827a authored by ffinfo's avatar ffinfo
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stringtie.wdl
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...@@ -5,7 +5,7 @@ import "common.wdl" ...@@ -5,7 +5,7 @@ import "common.wdl"
task Stringtie { task Stringtie {
input { input {
String? preCommand String? preCommand
IndexedBamFile bam IndexedBamFile bamFile
File? referenceGtf File? referenceGtf
Int threads = 1 Int threads = 1
String assembledTranscriptsFile String assembledTranscriptsFile
...@@ -25,7 +25,7 @@ task Stringtie { ...@@ -25,7 +25,7 @@ task Stringtie {
~{true="fr" false="" secondStranded} \ ~{true="fr" false="" secondStranded} \
-o ~{assembledTranscriptsFile} \ -o ~{assembledTranscriptsFile} \
~{"-A " + geneAbundanceFile} \ ~{"-A " + geneAbundanceFile} \
~{bam.file} ~{bamFile.file}
} }
output { output {
......
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