diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config index bd55d6a6ab5a546f68ce748ab20ff9795c9c5037..f3667f4f02d72675487ae9d4d73fab337110b53a 100644 --- a/src/nf_modules/htseq/htseq.config +++ b/src/nf_modules/htseq/htseq.config @@ -46,4 +46,30 @@ profiles { } } } + ccin2p3 { + process{ + withName: sort_bam { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" + cpus = 1 + memory = "10GB" + time = "24h" + } + withName: trimming { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/htseq/0.11.2/:/usr/bin:$PATH" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" + cpus = 1 + memory = "10GB" + time = "24h" + } + } + } }