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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} ${fq2} | ||
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} | ||
output { | ||
File tfq1 = "${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" | ||
} | ||
} | ||
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task dna_align { | ||
input { | ||
File fq1 | ||
File fq2 | ||
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} | ||
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} | ||
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workflow dna { | ||
inputs { | ||
File FqR1 | ||
File FqR2 | ||
String CID | ||
String SID | ||
String paneldir | ||
String refdir | ||
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} | ||
call trimseq { | ||
input: | ||
fq1=FqR1 | ||
fq2=FqR1 | ||
sampleid=SID | ||
} | ||
} |
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