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Merge branch 'master' of https://github.com/bcantarel/school
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Jeremy Mathews authored and Jeremy Mathews committed Dec 1, 2020
2 parents f4131d4 + 8617b16 commit 1527ba4
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48 changes: 48 additions & 0 deletions dna.wdl
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task trimseq {
input {
File fq1
File fq2
String sampleid
}
command {
bash ${repoDir}/process_scripts/preproc_fastq/trimgalore.sh -f -p ${sampleid} ${fq1} ${fq2}

}
output {
File tfq1 = "${sampleid}.trim.R1.fastq.gz"
File tfq2 = "${sampleid}.trim.R2.fastq.gz"
File treport = "${sampleid}.trimreport.txt"
}
runtime {
docker: "goalconsortium/trim_galore:1.0.7"
cpu: 1
memory: "4 GB"
}
}

task dna_align {
input {
File fq1
File fq2

}

}

workflow dna {
inputs {
File FqR1
File FqR2
String CID
String SID
String paneldir
String refdir

}
call trimseq {
input:
fq1=FqR1
fq2=FqR1
sampleid=SID
}
}
2 changes: 1 addition & 1 deletion nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ process {
singularity {
enabled = true
runOptions='--no-home --cleanenv'
cacheDir=$NXF_WORK
cacheDir="$PWD"
}

trace {
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