1 changed files with 5 additions and 4 deletions
+ 5
- 4
tasks/spladder_single.wdl
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| mkdir -p ${sample_id}/spladder_out | mkdir -p ${sample_id}/spladder_out | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| spladder build --bams ${bam} \ | spladder build --bams ${bam} \ | ||||
| --annotation ${reference_gtf_file} \ | --annotation ${reference_gtf_file} \ | ||||
| --ignore-mismatches \ | --ignore-mismatches \ | ||||
| --verbose \ | --verbose \ | ||||
| --confidence 2 \ | |||||
| --merge-strat single \ | --merge-strat single \ | ||||
| --sparse-bam \ | |||||
| --confidence 2 \ | |||||
| --readlen 150 \ | --readlen 150 \ | ||||
| --sparse-bam \ | |||||
| --parallel $nt \ | --parallel $nt \ | ||||
| --outdir ${sample_id}/spladder_out | |||||
| --outdir ${sample_id}/spladder_out | |||||
| find . -depth > fileList.txt | find . -depth > fileList.txt | ||||
| >>> | >>> |
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