3 changed files with 9 additions and 0 deletions
+ 2
- 0
tasks/fastqc.wdl
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| File read1 | File read1 | ||||
| File read2 | File read2 | ||||
| String docker | String docker | ||||
| String cluster | |||||
| String disk_size | |||||
| command <<< | command <<< | ||||
| set -o pipefail | set -o pipefail |
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tasks/fastqscreen.wdl
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| String read1name = basename(read1,".fastq.gz") | String read1name = basename(read1,".fastq.gz") | ||||
| String read2name = basename(read2,".fastq.gz") | String read2name = basename(read2,".fastq.gz") | ||||
| String docker | String docker | ||||
| String cluster | |||||
| String disk_size | |||||
| command <<< | command <<< | ||||
| set -o pipefail | set -o pipefail | ||||
| runtime { | runtime { | ||||
| docker:docker | docker:docker | ||||
| systemDisk:"cloud_ssd 40" | |||||
| cluster:cluster_config | |||||
| dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/" | |||||
| } | } | ||||
| output { | output { | ||||
| File png1 = "${read1name}_screen.png" | File png1 = "${read1name}_screen.png" |
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workflow.wdl
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| input: | input: | ||||
| read1=read1, | read1=read1, | ||||
| read2=read2, | read2=read2, | ||||
| cluster=cluster_config, | |||||
| docker=fastqc.docker | docker=fastqc.docker | ||||
| } | } | ||||
| input: | input: | ||||
| read1=read1, | read1=read1, | ||||
| read2=read2, | read2=read2, | ||||
| cluster=cluster_config, | |||||
| docker=fastqscreen.docker, | docker=fastqscreen.docker, | ||||
| screen_ref_dir=screen_ref_dir, | screen_ref_dir=screen_ref_dir, | ||||
| fastq_screen_conf=fastq_screen_conf | fastq_screen_conf=fastq_screen_conf |
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