From ebf51e72b507db34c7e7a31386540160b900e09b Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 7 May 2018 11:47:32 +0200
Subject: [PATCH] alphabetic ordering
---
biopet.wdl | 163 +++++++++++++++++++++++++++--------------------------
1 file changed, 83 insertions(+), 80 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 89293a9..054a166 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -1,3 +1,70 @@
+# PLEASE ADD TASKS IN ALPHABETIC ORDER.
+# This makes searching a lot easier.
+task BaseCounter {
+ String? preCommand
+ String tool_jar #Should this be of type File?
+ File bam
+ File refFlat
+ String outputDir
+ String prefix
+
+ Float? memory
+ Float? memoryMultiplier
+
+ Int mem = ceil(select_first([memory, 12.0]))
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ mkdir -p ${outputDir}
+ java -Xmx${mem}G -jar ${tool_jar} \
+ -b ${bam} \
+ -r ${refFlat} \
+ -o ${outputDir} \
+ -p ${prefix}
+ }
+
+ output {
+ File exonAntisense = outputDir + "/" + prefix + ".base.exon.antisense.counts"
+ File exon = outputDir + "/" + prefix + ".base.exon.counts"
+ File exonMergeAntisense = outputDir + "/" + prefix + ".base.exon.merge.antisense.counts"
+ File exonMerge = outputDir + "/" + prefix + ".base.exon.merge.counts"
+ File exonMergeSense = outputDir + "/" + prefix + ".base.exon.merge.sense.counts"
+ File exonSense = outputDir + "/" + prefix + ".base.exon.sense.counts"
+ File geneAntisense = outputDir + "/" + prefix + ".base.gene.antisense.counts"
+ File gene = outputDir + "/" + prefix + ".base.gene.counts"
+ File geneExonicAntisense = outputDir + "/" + prefix + ".base.gene.exonic.antisense.counts"
+ File geneExonic = outputDir + "/" + prefix + ".base.gene.exonic.counts"
+ File geneExonicSense = outputDir + "/" + prefix + ".base.gene.exonic.sense.counts"
+ File geneIntronicAntisense = outputDir + "/" + prefix + ".base.gene.intronic.antisense.counts"
+ File geneIntronic = outputDir + "/" + prefix + ".base.gene.intronic.counts"
+ File geneIntronicSense = outputDir + "/" + prefix + ".base.gene.intronic.sense.counts"
+ File geneSense = outputDir + "/" + prefix + ".base.gene.sense.counts"
+ File intronAntisense = outputDir + "/" + prefix + ".base.intron.antisense.counts"
+ File intron = outputDir + "/" + prefix + ".base.intron.counts"
+ File intronMergeAntisense = outputDir + "/" + prefix + ".base.intron.merge.antisense.counts"
+ File intronMerge = outputDir + "/" + prefix + ".base.intron.merge.counts"
+ File intronMergeSense = outputDir + "/" + prefix + ".base.intron.merge.sense.counts"
+ File intronSense = outputDir + "/" + prefix + ".base.intron.sense.counts"
+ File metaExonsNonStranded = outputDir + "/" + prefix + ".base.metaexons.non_stranded.counts"
+ File metaExonsStrandedAntisense = outputDir + "/" + prefix + ".base.metaexons.stranded.antisense.counts"
+ File metaExonsStranded = outputDir + "/" + prefix + ".base.metaexons.stranded.counts"
+ File metaExonsStrandedSense = outputDir + "/" + prefix + ".base.metaexons.stranded.sense.counts"
+ File transcriptAntisense = outputDir + "/" + prefix + ".base.transcript.antisense.counts"
+ File transcript = outputDir + "/" + prefix + ".base.transcript.counts"
+ File transcriptExonicAntisense = outputDir + "/" + prefix + ".base.transcript.exonic.antisense.counts"
+ File transcriptExonic = outputDir + "/" + prefix + ".base.transcript.exonic.counts"
+ File transcriptExonicSense = outputDir + "/" + prefix + ".base.transcript.exonic.sense.counts"
+ File transcriptIntronicAntisense = outputDir + "/" + prefix + ".base.transcript.intronic.antisense.counts"
+ File transcriptIntronic = outputDir + "/" + prefix + ".base.transcript.intronic.counts"
+ File transcriptIntronicSense = outputDir + "/" + prefix + ".base.transcript.intronic.sense.counts"
+ File transcriptSense = outputDir + "/" + prefix + ".base.transcript.sense.counts"
+ }
+
+ runtime {
+ memory: ceil(mem * select_first([memoryMultiplier, 1.5]))
+ }
+}
+
task FastqSplitter {
String? preCommand
File inputFastq
@@ -23,39 +90,6 @@ task FastqSplitter {
}
}
-task ScatterRegions {
- String? preCommand
- File ref_fasta
- File ref_dict
- String outputDirPath
- String tool_jar
- Int? scatterSize
- File? regions
-
- Float? memory
- Float? memoryMultiplier
-
- Int mem = ceil(select_first([memory, 4.0]))
- command {
- set -e -o pipefail
- ${preCommand}
- mkdir -p ${outputDirPath}
- java -Xmx${mem}G -jar ${tool_jar} \
- -R ${ref_fasta} \
- -o ${outputDirPath} \
- ${"-s " + scatterSize} \
- ${"-L " + regions}
- }
-
- output {
- Array[File] scatters = glob(outputDirPath + "/scatter-*.bed")
- }
-
- runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
- }
-}
-
task SampleConfig {
String? preCommand
String tool_jar
@@ -95,67 +129,36 @@ task SampleConfig {
}
}
-task BaseCounter {
+task ScatterRegions {
String? preCommand
- String tool_jar #Should this be of type File?
- File bam
- File refFlat
- String outputDir
- String prefix
+ File ref_fasta
+ File ref_dict
+ String outputDirPath
+ String tool_jar
+ Int? scatterSize
+ File? regions
Float? memory
Float? memoryMultiplier
- Int mem = ceil(select_first([memory, 12.0]))
+ Int mem = ceil(select_first([memory, 4.0]))
command {
set -e -o pipefail
${preCommand}
- mkdir -p ${outputDir}
+ mkdir -p ${outputDirPath}
java -Xmx${mem}G -jar ${tool_jar} \
- -b ${bam} \
- -r ${refFlat} \
- -o ${outputDir} \
- -p ${prefix}
+ -R ${ref_fasta} \
+ -o ${outputDirPath} \
+ ${"-s " + scatterSize} \
+ ${"-L " + regions}
}
output {
- File exonAntisense = outputDir + "/" + prefix + ".base.exon.antisense.counts"
- File exon = outputDir + "/" + prefix + ".base.exon.counts"
- File exonMergeAntisense = outputDir + "/" + prefix + ".base.exon.merge.antisense.counts"
- File exonMerge = outputDir + "/" + prefix + ".base.exon.merge.counts"
- File exonMergeSense = outputDir + "/" + prefix + ".base.exon.merge.sense.counts"
- File exonSense = outputDir + "/" + prefix + ".base.exon.sense.counts"
- File geneAntisense = outputDir + "/" + prefix + ".base.gene.antisense.counts"
- File gene = outputDir + "/" + prefix + ".base.gene.counts"
- File geneExonicAntisense = outputDir + "/" + prefix + ".base.gene.exonic.antisense.counts"
- File geneExonic = outputDir + "/" + prefix + ".base.gene.exonic.counts"
- File geneExonicSense = outputDir + "/" + prefix + ".base.gene.exonic.sense.counts"
- File geneIntronicAntisense = outputDir + "/" + prefix + ".base.gene.intronic.antisense.counts"
- File geneIntronic = outputDir + "/" + prefix + ".base.gene.intronic.counts"
- File geneIntronicSense = outputDir + "/" + prefix + ".base.gene.intronic.sense.counts"
- File geneSense = outputDir + "/" + prefix + ".base.gene.sense.counts"
- File intronAntisense = outputDir + "/" + prefix + ".base.intron.antisense.counts"
- File intron = outputDir + "/" + prefix + ".base.intron.counts"
- File intronMergeAntisense = outputDir + "/" + prefix + ".base.intron.merge.antisense.counts"
- File intronMerge = outputDir + "/" + prefix + ".base.intron.merge.counts"
- File intronMergeSense = outputDir + "/" + prefix + ".base.intron.merge.sense.counts"
- File intronSense = outputDir + "/" + prefix + ".base.intron.sense.counts"
- File metaExonsNonStranded = outputDir + "/" + prefix + ".base.metaexons.non_stranded.counts"
- File metaExonsStrandedAntisense = outputDir + "/" + prefix + ".base.metaexons.stranded.antisense.counts"
- File metaExonsStranded = outputDir + "/" + prefix + ".base.metaexons.stranded.counts"
- File metaExonsStrandedSense = outputDir + "/" + prefix + ".base.metaexons.stranded.sense.counts"
- File transcriptAntisense = outputDir + "/" + prefix + ".base.transcript.antisense.counts"
- File transcript = outputDir + "/" + prefix + ".base.transcript.counts"
- File transcriptExonicAntisense = outputDir + "/" + prefix + ".base.transcript.exonic.antisense.counts"
- File transcriptExonic = outputDir + "/" + prefix + ".base.transcript.exonic.counts"
- File transcriptExonicSense = outputDir + "/" + prefix + ".base.transcript.exonic.sense.counts"
- File transcriptIntronicAntisense = outputDir + "/" + prefix + ".base.transcript.intronic.antisense.counts"
- File transcriptIntronic = outputDir + "/" + prefix + ".base.transcript.intronic.counts"
- File transcriptIntronicSense = outputDir + "/" + prefix + ".base.transcript.intronic.sense.counts"
- File transcriptSense = outputDir + "/" + prefix + ".base.transcript.sense.counts"
+ Array[File] scatters = glob(outputDirPath + "/scatter-*.bed")
}
runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 1.5]))
+ memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
}
}
+
--
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