3 changed files with 2 additions and 3 deletions
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tasks/ballgown.wdl
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| @@ -1,10 +1,10 @@ | |||
| task ballgown { | |||
| File gene_abundance | |||
| String base=basename(gene_abundance, ".gene.abundance.txt") | |||
| Array[File] ballgown | |||
| String docker | |||
| String cluster | |||
| String disk_size | |||
| Array[File] ballgown | |||
| command <<< | |||
| mkdir -p /cromwell_root/tmp/${base} | |||
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tasks/fastp.wdl
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| @@ -1,7 +1,7 @@ | |||
| task fastp { | |||
| String sample_id | |||
| File read1 | |||
| File read2 | |||
| String sample_id | |||
| String adapter_sequence | |||
| String adapter_sequence_r2 | |||
| String docker | |||
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workflow.wdl
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| @@ -2,7 +2,6 @@ import "./tasks/fastqc.wdl" as fastqc | |||
| import "./tasks/fastqscreen.wdl" as fastqscreen | |||
| import "./tasks/fastp.wdl" as fastp | |||
| import "./tasks/qualimap.wdl" as qualimap | |||
| import "./tasks/hisat2_fp.wdl" as hisat2_fp | |||
| import "./tasks/hisat2.wdl" as hisat2 | |||
| import "./tasks/samtools.wdl" as samtools | |||
| import "./tasks/stringtie.wdl" as stringtie | |||
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