From 9dde7d50cd4597f5f286c7fdf4d231033c8e5492 Mon Sep 17 00:00:00 2001
From: jboom1 <j.boom.me@lumc.nl>
Date: Thu, 22 Aug 2019 11:05:23 +0200
Subject: [PATCH] Add WDL task for TranscriptClean
---
transcriptclean.wdl | 199 ++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 199 insertions(+)
create mode 100644 transcriptclean.wdl
diff --git a/transcriptclean.wdl b/transcriptclean.wdl
new file mode 100644
index 0000000..84dc6a2
--- /dev/null
+++ b/transcriptclean.wdl
@@ -0,0 +1,199 @@
+version 1.0
+
+# Copyright (c) 2019 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task transcriptclean {
+ input {
+ File SAMfile
+ File referenceFile
+ String outputPrefix
+ String outputDirPath
+ File? spliceJnsFile
+ File? variantsFile
+ Int? maxLenIndel
+ Int? maxSJoffset
+ Boolean? correctMismatches
+ Boolean? correctIndels
+ Boolean? correctSJs
+ Boolean? dryRun
+ Boolean? primaryOnly
+ Int cores = 1
+ Int memory = 25
+ String dockerImage = "biocontainers/transcriptclean:v1.0.7_cv1"
+ }
+
+ command {
+ set -e pipefail
+ mkdir -p ~{outputDirPath}
+ TranscriptClean \
+ ~{"-s " + SAMfile} \
+ ~{"-g " + referenceFile} \
+ ~{"-o " + outputDirPath + outputPrefix} \
+ ~{"-j " + spliceJnsFile} \
+ ~{"-v " + variantsFile} \
+ ~{"--maxLenIndel=" + maxLenIndel} \
+ ~{"--maxSJOffset=" + maxSJoffset} \
+ ~{true="-m CORRECTMISMATCHES" false="-m false" correctMismatches} \
+ ~{true="-i CORRECTINDELS" false="-i false" correctIndels} \
+ ~{true="--correctSJs=CORRECTSJS" false="--correctSJs=false" correctSJs} \
+ ~{true="--dryRun" false="" dryRun} \
+ ~{true="--primaryOnly" false="" primaryOnly}
+ }
+
+ 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"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+}
+
+task cleansplicejns {
+ input{
+ File SAMfile
+ File referenceFile
+ String outputPrefix
+ String outputDirPath
+ File spliceJNsFile
+ File? variantsFile
+ Int cores = 1
+ Int memory = 4
+ String dockerImage = "biocontainers/transcriptclean:v1.0.7_cv1"
+ }
+
+ command {
+ set -e pipefail
+ mkdir -p ~{outputDirPath}
+ clean_splice_jns \
+ ~{"--f=" + SAMfile} \
+ ~{"--g=" + referenceFile} \
+ ~{"--o=" + outputDirPath + outputPrefix} \
+ ~{"--s=" + spliceJNsFile} \
+ ~{"--v=" + variantsFile}
+ }
+
+ output {
+ File outputCleanSJsam = outputDirPath + outputPrefix + "_clean.sam"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+}
+
+task getsjsfromgtf {
+ input {
+ File GTFfile
+ File referenceFile
+ String outputPrefix
+ String outputDirPath
+ Int? minIntronSize
+ Int cores = 1
+ Int memory = 8
+ String dockerImage = "biocontainers/transcriptclean:v1.0.7_cv1"
+ }
+
+ command {
+ set -e pipefail
+ mkdir -p ~{outputDirPath}
+ get_SJs_from_gtf \
+ ~{"--f=" + GTFfile} \
+ ~{"--g=" + referenceFile} \
+ ~{"--o=" + outputDirPath + outputPrefix + ".tsv"} \
+ ~{"--minIntronSize=" + minIntronSize}
+ }
+
+ output {
+ File outputSJsFile = outputDirPath + outputPrefix + ".tsv"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+}
+
+task getcorrectedsjsfromlog {
+ input{
+ File TElogFile
+ String outputPrefix
+ String outputDirPath
+ Int cores = 1
+ Int memory = 5
+ String dockerImage = "biocontainers/transcriptclean:v1.0.7_cv1"
+ }
+
+ command {
+ set -e pipefail
+ mkdir -p ~{outputDirPath}
+ get_corrected_SJs_from_log \
+ ~{TElogFile} \
+ ~{outputDirPath + outputPrefix + ".tsv"}
+ }
+
+ output {
+ File outputCorrectedSJs = outputDirPath + outputPrefix + ".tsv"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+}
+
+task gettranscriptcleanstats {
+ input{
+ File minimapSAMfile
+ String outputPrefix
+ String outputDirPath
+ Int cores = 1
+ Int memory = 4
+ String dockerImage = "biocontainers/transcriptclean:v1.0.7_cv1"
+ }
+
+ command {
+ set -e pipefail
+ mkdir -p ~{outputDirPath}
+ get_TranscriptClean_stats \
+ ~{minimapSAMfile} \
+ ~{outputDirPath + outputPrefix}
+ }
+
+ output {
+ File outputStat = stdout()
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+}
--
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