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