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remove fastp useless paramater

tags/v0.1.0
stead99 4 years ago
parent
commit
241ae9413a
1 changed files with 9 additions and 9 deletions
  1. +9
    -9
      tasks/fastp.wdl

+ 9
- 9
tasks/fastp.wdl View File

String trim_adapter String trim_adapter


command <<< command <<<
nt=$(nproc)
## Trim
if [ "${trim_adapter}" != 'true' ]; then
cp ${read1} ${sample_id}_R1.fq.gz
cp ${read2} ${sample_id}_R2.fq.gz
else
fastp --thread $nt --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe -i ${read1} -I ${read2} -o ${sample_id}_R1.fq.gz -O ${sample_id}_R2.fq.gz -j ${sample_id}.json -h ${sample_id}.html
fi
nt=$(nproc)
## Trim
if [ "${trim_adapter}" != 'true' ]; then
cp ${read1} ${sample_id}_R1.fq.gz
cp ${read2} ${sample_id}_R2.fq.gz
else
fastp --thread $nt --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe -i ${read1} -I ${read2} -o ${sample_id}_R1.fq.gz -O ${sample_id}_R2.fq.gz -j ${sample_id}.json -h ${sample_id}.html
fi
>>> >>>
runtime { runtime {

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