3 změnil soubory, kde provedl 2 přidání a 3 odebrání
+ 1
- 1
tasks/qualimap.wdl
Zobrazit soubor
| @@ -11,7 +11,7 @@ task qualimap { | |||
| set -e | |||
| nt=$(nproc) | |||
| /opt/qualimap/qualimap bamqc -bam ${bam} -outformat HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G | |||
| /opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -outdir ${bamname}_rnaseq -gtf ${gtf} -pe --java-mem-size=32G | |||
| /opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -outdir ${bamname}_rnaseq -gtf ${gtf} -pe -s --java-mem-size=32G | |||
| tar -zcf ${bamname}_bamqc_qualimap.tar.gz ${bamname}_bamqc | |||
| tar -zcf ${bamname}_rnaseq_qualimap.tar.gz ${bamname}_rnaseq | |||
+ 0
- 1
tasks/samtools.wdl
Zobrazit soubor
| @@ -26,7 +26,6 @@ task samtools { | |||
| } | |||
| output { | |||
| File out_unsort_bam=bam | |||
| File out_sort_bam=sorted_bam | |||
| File out_sort_bam_index=sorted_bam_index | |||
| File out_samstats=samstats | |||
+ 1
- 1
workflow.wdl
Zobrazit soubor
| @@ -83,7 +83,7 @@ workflow {{ project_name }} { | |||
| call qualimap.qualimap as qualimap { | |||
| input: | |||
| bam=samtools.out_unsort_bam, | |||
| bam=samtools.out_sort_bam, | |||
| gtf=gtf, | |||
| docker=qualimap_docker, | |||
| cluster=qualimap_cluster, | |||
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