1 changed files with 8 additions and 10 deletions
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- 10
tasks/fastp.wdl
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| String disk_size | String disk_size | ||||
| String out1_name = sample_id+'clean_1.fastq' | |||||
| String out2_name = sample_id+'clean_2.fastq' | |||||
| String out1_name = sample_id+'clean_1.fastq.gz' | |||||
| String out2_name = sample_id+'clean_2.fastq.gz' | |||||
| command <<< | command <<< | ||||
| set -o pipefail | |||||
| set -e | |||||
| nt=$(nproc) | |||||
| # basic command | # basic command | ||||
| /opt/conda/bin/fastp \ | /opt/conda/bin/fastp \ | ||||
| --in1 ${in1} \ | --in1 ${in1} \ | ||||
| --json ${json} \ | --json ${json} \ | ||||
| --html ${html} \ | --html ${html} \ | ||||
| --report_title ${report_title} \ | --report_title ${report_title} \ | ||||
| # options | |||||
| ${ true="--phred64 " false="" phred64 } \ | |||||
| ${ "--reads_to_process " + reads_to_process } \ | |||||
| ${ true="--fix_mgi_id " false="" fix_mgi_id } \ | |||||
| ${ "--adapter_sequence " + adapter_sequence } \ | |||||
| ${ "--adapter_sequence_r2 " + adapter_sequence_r2 } | |||||
| --thread $nt \ | |||||
| --length_required 30 | |||||
| >>> | >>> | ||||
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