1 changed files with 4 additions and 2 deletions
+ 4
- 2
tasks/spladder.wdl
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| set -e | set -e | ||||
| mkdir -p ${sample_id}/spladder_out | mkdir -p ${sample_id}/spladder_out | ||||
| nt=$(nproc) | |||||
| spladder build --bams ${bam} \ | spladder build --bams ${bam} \ | ||||
| --annotation ${reference_gtf_file} \ | --annotation ${reference_gtf_file} \ | ||||
| --ignore-mismatches \ | --ignore-mismatches \ | ||||
| --confidence 2 \ | --confidence 2 \ | ||||
| --readlen 150 \ | --readlen 150 \ | ||||
| --parallel 4 \ | |||||
| --parallel $nt \ | |||||
| --outdir ${sample_id}/spladder_out | --outdir ${sample_id}/spladder_out | ||||
| find . -depth > fileList.txt | find . -depth > fileList.txt |
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