1 changed files with 6 additions and 4 deletions
+ 6
- 4
tasks/fastqc.wdl
View File
| File read1 | File read1 | ||||
| File read2 | File read2 | ||||
| String docker | String docker | ||||
| String read1name=sub(basename(read1),"\\.\\S+$", "") | |||||
| String read2name=sub(basename(read2),"\\.\\S+$", "") | |||||
| String cluster | String cluster | ||||
| String disk_size | String disk_size | ||||
| dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" | dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" | ||||
| } | } | ||||
| output { | output { | ||||
| File read1_html=sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.html") | |||||
| File read1_zip=sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.zip") | |||||
| File read2_html=sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_fastqc.html") | |||||
| File read2_zip=sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_fastqc.zip") | |||||
| File read1_html="${read1name}_fastqc.html" | |||||
| File read1_zip="${read1name}_fastqc.zip" | |||||
| File read2_html="${read2name}_fastqc.html" | |||||
| File read2_zip="${read1name}_fastqc.zip" | |||||
| } | } | ||||
| } | } |
Loading…