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Unverified Commit 5d9cab2d authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
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Merge branch 'master' into splitNCigarReads

parents 817cb4ce 8155c98c
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1 merge request!5add SplitNCigarReads
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star.wdl
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...@@ -6,8 +6,8 @@ task Star { ...@@ -6,8 +6,8 @@ task Star {
String genomeDir String genomeDir
String outFileNamePrefix String outFileNamePrefix
String? outSAMtype = "BAM SortedByCoordinate" String? outSAMtype
String? readFilesCommand = "zcat" String? readFilesCommand
Int? runThreadN Int? runThreadN
String? outStd String? outStd
String? twopassMode String? twopassMode
...@@ -24,8 +24,8 @@ task Star { ...@@ -24,8 +24,8 @@ task Star {
--readFilesIn ${sep=',' inputR1} ${sep="," inputR2} \ --readFilesIn ${sep=',' inputR1} ${sep="," inputR2} \
--outFileNamePrefix ${outFileNamePrefix} \ --outFileNamePrefix ${outFileNamePrefix} \
--genomeDir ${genomeDir} \ --genomeDir ${genomeDir} \
${"--readFilesCommand " + readFilesCommand} \ --outSAMtype ${default="BAM SortedByCoordinate" outSAMtype} \
${"--outSAMtype " + outSAMtype} \ --readFilesCommand ${default="zcat" readFilesCommand} \
${"--runThreadN " + runThreadN} \ ${"--runThreadN " + runThreadN} \
${"--outStd " + outStd} \ ${"--outStd " + outStd} \
${"--twopassMode " + twopassMode} \ ${"--twopassMode " + twopassMode} \
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