1 changed files with 4 additions and 8 deletions
+ 4
- 8
tasks/rmats.wdl
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| task rmats { | task rmats { | ||||
| String sample_id | String sample_id | ||||
| File b1_1 | |||||
| File b1_2 | |||||
| File b1_3 | |||||
| File b2_1 | |||||
| File b2_2 | |||||
| File b2_3 | |||||
| File b1_txt | |||||
| File b2_txt | |||||
| File reference_gtf_file | File reference_gtf_file | ||||
| mkdir -p ${sample_id}/output | mkdir -p ${sample_id}/output | ||||
| mkdir -p ${sample_id}/tmp_output | mkdir -p ${sample_id}/tmp_output | ||||
| python /usr/local/bin/rmats.py --b1 ${b1_1},${b1_2},${b1_3} \ | |||||
| --b2 ${b2_1},${b2_2},${b2_3}\ | |||||
| python /usr/local/bin/rmats.py --b1 ${b1_txt} \ | |||||
| --b2 ${b2_txt} \ | |||||
| --gtf ${reference_gtf_file} \ | --gtf ${reference_gtf_file} \ | ||||
| -t paired \ | -t paired \ | ||||
| --readLength 150 \ | --readLength 150 \ |
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