diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config index 06c3fcc5ea2074ee69b44ccf96167581b7afec2f..dd88348a0aa63f72a3f3c08e7cdc2472596fa9f6 100644 --- a/src/nf_modules/sambamba/index_bams.config +++ b/src/nf_modules/sambamba/index_bams.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: index_bam { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$PATH" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" + cpus = 1 + memory = "10GB" + time = "24h" + } + } + } } diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config index 73f2bcd16faf8a52847acb3061dbfcc96f45c029..fe605cf4bc9ed80cf1a0abe0b18d2da8a6b90579 100644 --- a/src/nf_modules/sambamba/sort_bams.config +++ b/src/nf_modules/sambamba/sort_bams.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: sort_bam { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$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" + } + } + } } diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config index 95173ec226c71587b30f62a015fbf45bc0d34279..087a0dd57e9c1135483332e4e728eebdd806e799 100644 --- a/src/nf_modules/sambamba/split_bams.config +++ b/src/nf_modules/sambamba/split_bams.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: split_bam { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/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" + } + } + } }