1 changed files with 2 additions and 2 deletions
+ 2
- 2
tasks/fastqscreen.wdl
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| @@ -13,8 +13,8 @@ task fastq_screen { | |||
| nt=$(nproc) | |||
| mkdir -p /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} --subset 1000000 --threads $nt ${read1} | |||
| fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --subset 1000000 --threads $nt ${read2} | |||
| >>> | |||
| runtime { | |||
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