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tasks/arcashla.wdl
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| command <<< | command <<< | ||||
| mkdir hla_type | 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 { | runtime { |
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