1 changed files with 2 additions and 2 deletions
+ 2
- 2
tasks/arcashla.wdl
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| @@ -6,8 +6,8 @@ task arcashla { | |||
| command <<< | |||
| mkdir hla_type | |||
| /opt/conda/bin/arcasHLA extract ${bam} -o ${base}.extracted.fq.gz --paired -t 8 -v | |||
| /opt/conda/bin/arcasHLA genotype ${base}.extracted.1.fq.gz ${base}.extracted.2.fq.gz hla_type/${base}.genotype.json | |||
| ./arcasHLA/arcasHLA extract ${bam} -o ${base}.extracted.fq.gz --paired -t 8 -v | |||
| ./arcasHLA/arcasHLA genotype ${base}.extracted.1.fq.gz ${base}.extracted.2.fq.gz hla_type/${base}.genotype.json | |||
| >>> | |||
| runtime { | |||
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