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tasks/rmats.wdl
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| task rmats { | task rmats { | ||||
| String sample_id | String sample_id | ||||
| File b1_txt_file | |||||
| File b1_txt_file ## 阿里云不能直接读取txt内容，要建立阿里云和服务器的联系（read_csv） | |||||
| Array[Array[File]] b1_txt = read_csv(b1_txt_file) | Array[Array[File]] b1_txt = read_csv(b1_txt_file) | ||||
| File b2_txt_file | File b2_txt_file | ||||
| Array[Array[File]] b2_txt = read_csv(b2_txt_file) | Array[Array[File]] b2_txt = read_csv(b2_txt_file) | ||||
| mkdir -p ${sample_id}/output | mkdir -p ${sample_id}/output | ||||
| mkdir -p ${sample_id}/tmp_output | mkdir -p ${sample_id}/tmp_output | ||||
| ### 命令行无需修改 | |||||
| python /usr/local/bin/rmats.py --b1 ${b1_txt} \ | python /usr/local/bin/rmats.py --b1 ${b1_txt} \ | ||||
| --b2 ${b2_txt} \ | --b2 ${b2_txt} \ | ||||
| --gtf ${reference_gtf_file} \ | --gtf ${reference_gtf_file} \ |
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