WDL script for adapter trimming
Answers
Answer:
WDL script for adapter trimming A shopkeeper announced two successive discount 20% and 10% on purchasing of ...
Answer:
task trimsequencesTask {
File InputRead1
String InputRead2
String SampleName
File Adapters
String CutAdapt
String CutAdaptThreads
Boolean PairedEnd
File TrimSeqScript
File TrimEnvProfile
String DebugMode
command {
/bin/bash ${TrimSeqScript} -P ${PairedEnd} -l
${InputRead1} -r ${InputRead2} -s ${SampleName} -A ${Adapters} -C ${CutAdapt} -t
${CutAdaptThreads} -e ${TrimEnvProfile} ${DebugMode}
}
output {
File TrimmedInputRead1 = "${SampleName}.read1.trimmed.fq.gz"
File TrimmedInputRead2 = "${SampleName}.read2.trimmed.fq.gz"
}
}
Explanation:
WDL stands for World Definition Language Script.
How to write WDL script :
Open a blank text file in your favorite text editor and save the file as Any_name.wdl.
(Note the wdl file extension--your text editor might tell you to use txt,
which won’t work.) Both the workflow and the tasks will be written to this file.
Below are script options for above script.
## Script Options
# -t "Number of Threads" (Required)
# -P "Single Ended Reads specification" (Required)
# -r "Left Fast_q File" (Required)
# -R "Right Fast_q File" (Optional)
# -s "Name of the sample" (Optional)
# -A "Adapter File for Cut_Adapter" (Required)
# -C "Path to Cut_Adapter Tool" (Required)
# -e "Path to the environmental profile (Required)
# -d "debug mode on/off (Optional: can be empty)