1 changed files with 2 additions and 2 deletions
+ 2
- 2
tasks/fastqscreen.wdl
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| nt=$(nproc) | nt=$(nproc) | ||||
| mkdir -p /cromwell_root/tmp | mkdir -p /cromwell_root/tmp | ||||
| cp -r ${screen_ref_dir} /cromwell_root/tmp/ | cp -r ${screen_ref_dir} /cromwell_root/tmp/ | ||||
| fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read1} | |||||
| fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read2} | |||||
| fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read1} --outdir ./ | |||||
| fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read2} --outdir ./ | |||||
| >>> | >>> | ||||
| runtime { | runtime { |
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