diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config index cae101a51a4adc1f118d7321aa92db9d1630156a..a6e6d9fe38e87a692f606bca6568c51a613cd5bf 100644 --- a/src/nf_modules/bwa/indexing.config +++ b/src/nf_modules/bwa/indexing.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: index_fasta { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bwa/0.7.17/:/usr/bin:$PATH" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" + cpus = 1 + memory = "10GB" + time = "24h" + } + } + } } diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config index e3ff6728be10872184b86554afdaf563891b41df..d583ff1cbaa45f8853e43fef543e8e2daf0c44ce 100644 --- a/src/nf_modules/bwa/mapping_paired.config +++ b/src/nf_modules/bwa/mapping_paired.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: mapping_fastq { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bwa/0.7.17/:/usr/bin:$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" + } + } + } }