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tasks/arcashla.wdl
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| String base = basename(bam, ".sorted.bam") | String base = basename(bam, ".sorted.bam") | ||||
| String docker | String docker | ||||
| String cluster | String cluster | ||||
| String disk_size | |||||
| command <<< | command <<< | ||||
| mkdir hla_type | mkdir hla_type |
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tasks/hisat2.wdl
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| String base = sub(basename(read_1P),"\\.\\S+$", "") | String base = sub(basename(read_1P),"\\.\\S+$", "") | ||||
| String docker | String docker | ||||
| String cluster | String cluster | ||||
| String disk_size | |||||
| command { | command { | ||||
| nt=$(nproc) | nt=$(nproc) |
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tasks/samtools.wdl
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| String sorted_bam_index = base + ".sorted.bam.bai" | String sorted_bam_index = base + ".sorted.bam.bai" | ||||
| String docker | String docker | ||||
| String cluster | String cluster | ||||
| String disk_size | |||||
| command <<< | command <<< | ||||
| set -o pipefail | set -o pipefail |
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