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defaults
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| @@ -1,6 +1,6 @@ | |||
| { | |||
| "gtf": "oss://pgx-reference-data/reference/tophat2/annotation/gencode.v22.annotation.gtf", | |||
| "genome_directory":"oss://pgx-reference-data/reference/tophat2/genome", | |||
| "genome_directory":"oss://pgx-reference-data/reference/tophat2/genome/", | |||
| "idx_prefix":"tophat2", | |||
| "adapter": "oss://pgx-reference-data/reference/illumina_adapter/TruSeq3-PE.fa", | |||
| "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5", | |||
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tasks/tophat2.wdl
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| @@ -9,7 +9,7 @@ task tophat2 { | |||
| String cluster | |||
| command <<< | |||
| tophat -p 6 -G ${gtf} --library-type fr-unstranded --solexa-quals -o ${baseout} ${genome_directory}/${idx_prefix} ${read1} ${read2} | |||
| tophat2 -p 6 -G ${gtf} --library-type fr-unstranded --solexa-quals -o ${baseout} ${genome_directory}/${idx_prefix} ${read1} ${read2} | |||
| >>> | |||
| runtime { | |||
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