2 changed files with 2 additions and 4 deletions
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inputs
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| "{{ project_name }}.bed_file": "oss://pgx-reference-data/reference/bedtools/ERVmap_v2_all_sorted.bed", | "{{ project_name }}.bed_file": "oss://pgx-reference-data/reference/bedtools/ERVmap_v2_all_sorted.bed", | ||||
| "{{ project_name }}.bedtools.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc", | "{{ project_name }}.bedtools.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc", | ||||
| "{{ project_name }}.bedtools.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1", | "{{ project_name }}.bedtools.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1", | ||||
| "{{ project_name }}.bedtools.disk_size": "100" | |||||
| "{{ project_name }}.bedtools.disk_size": "{{disk_size}}" | |||||
| } | } |
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tasks/bedtools.wdl
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| String disk_size | String disk_size | ||||
| command <<< | command <<< | ||||
| set -o pipefail | |||||
| set -e | |||||
| bedtools multicov -bams ${bam} -bed ${bed_file} > revread_count.txt | bedtools multicov -bams ${bam} -bed ${bed_file} > revread_count.txt | ||||
| >>> | >>> |
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