63 lines
1.7 KiB
Plaintext
63 lines
1.7 KiB
Plaintext
task runqc {
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String name
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String inputDir
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String outputDir
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command <<<
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echo "###### ${name} fastp beginning at: $(date) ######"
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if [ ! -d ${outputDir}/qc ];then
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mkdir ${outputDir}/qc
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fi
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fastp -i ${inputDir}/*_${name}_*1.fq.gz -o ${outputDir}/qc/${name}_clean_R1.fq.gz \
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-I ${inputDir}/*_${name}_*2.fq.gz -O ${outputDir}/qc/${name}_clean_R2.fq.gz \
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-w 10 \
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--correction \
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--overlap_len_require 10 \
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-j ${outputDir}/qc/${name}.json \
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-h ${outputDir}/qc/${name}.html \
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--report_title $name \
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-e 20
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echo "###### ${name} fastp end at: $(date) ######"
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>>>
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output {
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String r1 = "${outputDir}/qc/${name}_clean_R1.fq.gz "
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String r2 = "${outputDir}/qc/${name}_clean_R2.fq.gz "
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String json = "${outputDir}/qc/${name}.json"
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}
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}
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workflow qc {
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String tumor
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String? normal
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String inputDir
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String outputDir
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scatter(name in [tumor, normal]) {
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if (defined(name)) {
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call runqc {
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input:
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name=name,
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inputDir=inputDir,
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outputDir=outputDir
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}
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}
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}
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output {
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String tumor_r1 = "${outputDir}/qc/${tumor}_clean_R1.fq.gz "
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String tumor_r2 = "${outputDir}/qc/${tumor}_clean_R2.fq.gz "
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String tumor_json = "${outputDir}/qc/${tumor}.json"
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String normal_r1 = "${outputDir}/qc/${normal}_clean_R1.fq.gz "
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String normal_r2 = "${outputDir}/qc/${normal}_clean_R2.fq.gz "
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String normal_json = "${outputDir}/qc/${normal}.json"
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}
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}
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