From f9bbb353a1c133fc30ae2db6b2fcfeb69c4b7547 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 9 Nov 2018 15:57:49 +0100
Subject: [PATCH] continue on task
---
gffcompare.wdl | 23 +++++++++++++++++++++--
1 file changed, 21 insertions(+), 2 deletions(-)
diff --git a/gffcompare.wdl b/gffcompare.wdl
index 7f69ce8..a60ce6f 100644
--- a/gffcompare.wdl
+++ b/gffcompare.wdl
@@ -24,11 +24,15 @@ task GffCompare {
Boolean noTmap = false
Boolean verbose = false
Boolean debugMode = false
+ # This workaround only works in the input section.
+ # Issue addressed at https://github.com/openwdl/wdl/pull/263
+ File? noneFile # This is a wdl workaround. Please do not assign!
}
# This allows for the creation of output directories"
String dirPrefix= if defined(outputDir) then outputDir + "/" else ""
String totalPrefix = dirPrefix + outPrefix
+
parameter_meta {}
command {
@@ -37,7 +41,7 @@ task GffCompare {
~{"mkdir -p " + outputDir}
gffcompare \
-r ~{referenceAnnotation} \
- ~{"-o " + totalPrefix } \
+ ~{"-o '" + totalPrefix + "'"} \
~{"-s " + genomeSequences} \
~{"-e " + maxDistanceFreeEndsTerminalExons} \
~{"-d " + maxDistanceGroupingTranscriptStartSites} \
@@ -57,5 +61,20 @@ task GffCompare {
~{sep=" " + inputGtfFiles}
}
- output {}
+ # Output of gffcompare is not stable. It depends on the number of files in the input.
+ Int noFilesGtfList = if defined(inputGtfList) then length(read_lines(inputGtfList)) else 0
+ Int noInputFiles = if defined(inputGtfFiles) then length(inputGtfFiles) else 0
+ Boolean oneFile = (noFilesGtfList + noInputFiles) == 1
+ String annotatedName = if oneFile then "annotated" else "combined"
+
+ # Check if a redundant .gtf will be created
+ Boolean createRedundant = C || A || X
+
+ output {
+ File annotated = totalPrefix + "." + annotatedName + ".gtf"
+ File loci = totalPrefix + ".loci"
+ File stats = totalPrefix + ".stats"
+ File tracking = totalPrefix + ".tracking"
+ File? redundant = if createRedundant then totalPrefix + ".redundant.gtf" else noneFile
+ }
}
\ No newline at end of file
--
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