1 changed files with 2 additions and 5 deletions
+ 2
- 5
tasks/qualimap.wdl
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| set -e | set -e | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| /opt/qualimap/qualimap bamqc -bam ${bam} -gff ${bed} -nt $nt -outdir ./ --java-mem-size=16G | /opt/qualimap/qualimap bamqc -bam ${bam} -gff ${bed} -nt $nt -outdir ./ --java-mem-size=16G | ||||
| zip -r qualimap.zip ./ | |||||
| >>> | >>> | ||||
| runtime { | runtime { | ||||
| } | } | ||||
| output { | output { | ||||
| File qualimap_txt = "genome_results.txt" | |||||
| Array[File] qualimap_images = glob("images_qualimapReport/*") | |||||
| File qualimap_html = "qualimapReport.html" | |||||
| Array[File] qulimap_raw_data = glob("raw_data_qualimapReport/*") | |||||
| Array[File] css = glob("css/*") | |||||
| File qualimap = "qualimap.zip" | |||||
| } | } | ||||
| } | } |
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