diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config index 2b3a814aeeb8a98e79c4018876ecb5cf6d123ab7..c8bab8dbf6c4a45d29029dbe8975a25f46757b6d 100644 --- a/src/nf_modules/samtools/filter_bams.config +++ b/src/nf_modules/samtools/filter_bams.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: filter_bam { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" + cpus = 1 + memory = "10GB" + time = "24h" + } + } + } } diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config index 5cec951ba634f96dbca2aa121497b2df57a11cfb..89c223b4f0a6a694c7257f58d5de867f9043bc8e 100644 --- a/src/nf_modules/samtools/index_bams.config +++ b/src/nf_modules/samtools/index_bams.config @@ -32,4 +32,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: index_bam { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$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" + } + } + } } diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config index 9f420077d2877a8d4f89873d835ebe0e703b640d..6d30cc5bdff88ab781705274c24a1b986867bfdc 100644 --- a/src/nf_modules/samtools/sort_bams.config +++ b/src/nf_modules/samtools/sort_bams.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: sort_bam { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" + cpus = 1 + memory = "10GB" + time = "24h" + } + } + } } diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config index 91b2f1ac1c69bc9ec8788f0db291a16cbfb96e73..9cd8b166eb4038b57d25fb42faa28cc80711537f 100644 --- a/src/nf_modules/samtools/split_bams.config +++ b/src/nf_modules/samtools/split_bams.config @@ -32,4 +32,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: split_bam { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$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" + } + } + } }