From bb9217dc32975440cf70eac3a479bcde98ad8fd5 Mon Sep 17 00:00:00 2001
From: jboom1 <j.boom.me@lumc.nl>
Date: Wed, 4 Sep 2019 13:38:20 +0200
Subject: [PATCH] Combined outputDirPath and outputPrefix to outputPrefix and
changed optional inputs with a default value to non optional
---
transcriptclean.wdl | 92 +++++++++++++++++++++++----------------------
1 file changed, 48 insertions(+), 44 deletions(-)
diff --git a/transcriptclean.wdl b/transcriptclean.wdl
index c0edeca..3870e68 100644
--- a/transcriptclean.wdl
+++ b/transcriptclean.wdl
@@ -20,12 +20,26 @@ version 1.0
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
+workflow test {
+ input {
+ File GTFfile
+ File genomeFile
+ String outputPrefix
+ }
+
+ call GetSJsFromGtf as GTFgen {
+ input:
+ GTFfile = GTFfile,
+ genomeFile = genomeFile,
+ outputPrefix = outputPrefix
+ }
+}
+
task CleanSpliceJunctions {
input {
File SAMfile
File referenceGenome
String outputPrefix
- String outputDirPath
File spliceJunctionAnnotation
File? variantFile
@@ -37,17 +51,17 @@ task CleanSpliceJunctions {
command {
set -e pipefail
- mkdir -p ~{outputDirPath}
+ mkdir -p $(dirname ~{outputPrefix})
clean_splice_jns \
~{"--f=" + SAMfile} \
~{"--g=" + referenceGenome} \
- ~{"--o=" + outputDirPath + outputPrefix} \
+ ~{"--o=" + outputPrefix} \
~{"--s=" + spliceJunctionAnnotation} \
~{"--v=" + variantFile}
}
output {
- File outputCleanedSAM = outputDirPath + outputPrefix + "_clean.sam"
+ File outputCleanedSAM = outputPrefix + "_clean.sam"
}
runtime {
@@ -59,8 +73,7 @@ task CleanSpliceJunctions {
parameter_meta {
SAMfile: "Input SAM file"
referenceGenome: "Reference genome fasta file."
- outputPrefix: "Output file prefix."
- outputDirPath: "Output directory path."
+ outputPrefix: "Output directory path + output file prefix."
spliceJunctionAnnotation: "Splice junction file"
variantFile: "VCF formatted file of variants"
@@ -72,7 +85,6 @@ task GetCorrectedSJsFromLog {
input {
File TElogFile
String outputPrefix
- String outputDirPath
Int cores = 1
Int memory = 5
@@ -81,14 +93,14 @@ task GetCorrectedSJsFromLog {
command {
set -e pipefail
- mkdir -p ~{outputDirPath}
+ mkdir -p $(dirname ~{outputPrefix})
get_corrected_SJs_from_log \
~{TElogFile} \
- ~{outputDirPath + outputPrefix + ".tsv"}
+ ~{outputPrefix + ".tsv"}
}
output {
- File outputCorrectedSJs = outputDirPath + outputPrefix + ".tsv"
+ File outputCorrectedSJs = outputPrefix + ".tsv"
}
runtime {
@@ -99,8 +111,7 @@ task GetCorrectedSJsFromLog {
parameter_meta {
TElogFile: "TE log from TranscriptClean."
- outputPrefix: "Output file prefix."
- outputDirPath: "Output directory path."
+ outputPrefix: "Output directory path + output file prefix."
outputCorrectedSJs: "Formely noncanonical splice junctions in BED format."
}
@@ -111,9 +122,7 @@ task GetSJsFromGtf {
File GTFfile
File genomeFile
String outputPrefix
- String outputDirPath
-
- Int? minIntronSize = 21
+ Int minIntronSize = 21
Int cores = 1
Int memory = 8
@@ -122,16 +131,16 @@ task GetSJsFromGtf {
command {
set -e pipefail
- mkdir -p ~{outputDirPath}
+ mkdir -p $(dirname ~{outputPrefix})
get_SJs_from_gtf \
~{"--f=" + GTFfile} \
~{"--g=" + genomeFile} \
- ~{"--o=" + outputDirPath + outputPrefix + ".tsv"} \
+ ~{"--o=" + outputPrefix + ".tsv"} \
~{"--minIntronSize=" + minIntronSize}
}
output {
- File outputSJsFile = outputDirPath + outputPrefix + ".tsv"
+ File outputSJsFile = outputPrefix + ".tsv"
}
runtime {
@@ -143,8 +152,7 @@ task GetSJsFromGtf {
parameter_meta {
GTFfile: "Input GTF file"
genomeFile: "Reference genome"
- outputPrefix: "Output file prefix."
- outputDirPath: "Output directory path."
+ outputPrefix: "Output directory path + output file prefix."
minIntronSize: "Minimum size of intron to consider a junction."
outputSJsFile: "Extracted splice junctions."
@@ -155,7 +163,6 @@ task GetTranscriptCleanStats {
input {
File transcriptCleanSAMfile
String outputPrefix
- String outputDirPath
Int cores = 1
Int memory = 4
@@ -164,10 +171,10 @@ task GetTranscriptCleanStats {
command {
set -e pipefail
- mkdir -p ~{outputDirPath}
+ mkdir -p $(dirname ~{outputPrefix})
get_TranscriptClean_stats \
~{transcriptCleanSAMfile} \
- ~{outputDirPath + outputPrefix}
+ ~{outputPrefix}
}
output {
@@ -182,8 +189,7 @@ task GetTranscriptCleanStats {
parameter_meta {
transcriptCleanSAMfile: "Output SAM file from TranscriptClean"
- outputPrefix: "Output file prefix."
- outputDirPath: "Output directory path."
+ outputPrefix: "Output directory path + output file prefix."
outputStatsFile: "Summary stats from TranscriptClean run."
}
@@ -194,17 +200,16 @@ task TranscriptClean {
File SAMfile
File referenceGenome
String outputPrefix
- String outputDirPath
+ Int maxLenIndel = 5
+ Int maxSJoffset = 5
+ Boolean correctMismatches = true
+ Boolean correctIndels = true
+ Boolean dryRun = false
+ Boolean primaryOnly = false
File? spliceJunctionAnnotation
File? variantFile
- Int? maxLenIndel = 5
- Int? maxSJoffset = 5
- Boolean? correctMismatches = true
- Boolean? correctIndels = true
Boolean? correctSJs
- Boolean? dryRun = false
- Boolean? primaryOnly = false
Int cores = 1
Int memory = 25
@@ -213,11 +218,11 @@ task TranscriptClean {
command {
set -e pipefail
- mkdir -p ~{outputDirPath}
+ mkdir -p $(dirname ~{outputPrefix})
TranscriptClean \
~{"-s " + SAMfile} \
~{"-g " + referenceGenome} \
- ~{"-o " + outputDirPath + outputPrefix} \
+ ~{"-o " + outputPrefix} \
~{"-j " + spliceJunctionAnnotation} \
~{"-v " + variantFile} \
~{"--maxLenIndel=" + maxLenIndel} \
@@ -230,10 +235,10 @@ task TranscriptClean {
}
output {
- File outputTcFasta = outputDirPath + outputPrefix + "_clean.fa"
- File outputTcLog = outputDirPath + outputPrefix + "_clean.log"
- File outputTcSAM = outputDirPath + outputPrefix + "_clean.sam"
- File outputTcTElog = outputDirPath + outputPrefix + "_clean.TE.log"
+ File outputTranscriptCleanFasta = outputPrefix + "_clean.fa"
+ File outputTranscriptCleanLog = outputPrefix + "_clean.log"
+ File outputTranscriptCleanSAM = outputPrefix + "_clean.sam"
+ File outputTranscriptCleanTElog = outputPrefix + "_clean.TE.log"
}
runtime {
@@ -245,8 +250,7 @@ task TranscriptClean {
parameter_meta {
SAMfile: "Input SAM file containing transcripts to correct."
referenceGenome: "Reference genome fasta file."
- outputPrefix: "Output file prefix."
- outputDirPath: "Output directory path."
+ outputPrefix: "Output directory path + output file prefix."
spliceJunctionAnnotation: "Splice junction file"
maxLenIndel: "Maximum size indel to correct."
maxSJoffset: "Maximum distance from annotated splice junction to correct."
@@ -256,9 +260,9 @@ task TranscriptClean {
dryRun: "TranscriptClean will read in the data but don't do any correction."
primaryOnly: "TranscriptClean will only output primary mappings of transcripts."
- outputTcFasta: "Fasta file containing corrected reads."
- outputTcLog: "Log file of TranscriptClean run."
- outputTcSAM: "SAM file containing corrected aligned reads."
- outputTcTElog: "TE log file of TranscriptClean run."
+ outputTranscriptCleanFasta: "Fasta file containing corrected reads."
+ outputTranscriptCleanLog: "Log file of TranscriptClean run."
+ outputTranscriptCleanSAM: "SAM file containing corrected aligned reads."
+ outputTranscriptCleanTElog: "TE log file of TranscriptClean run."
}
}
--
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