diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config index c55891bc0258987c293bad3255620b994ce12644..10c4ac96364c0093537f963b9b565c16e769465a 100644 --- a/src/nf_modules/bowtie/indexing.config +++ b/src/nf_modules/bowtie/indexing.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: index_fasta { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie/1.2.2/:/usr/bin:$PATH" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" + cpus = 1 + memory = "10GB" + time = "24h" + } + } + } } diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config index 28ce647adc1887832efb0035b9c59adce4bb8307..f531d0dcedcfce5e6233e0f41d4a2f43c9810fbb 100644 --- a/src/nf_modules/bowtie/mapping_paired.config +++ b/src/nf_modules/bowtie/mapping_paired.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: mapping_fastq { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie/1.2.2/:/usr/bin:$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" + } + } + } } diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config index 28ce647adc1887832efb0035b9c59adce4bb8307..f531d0dcedcfce5e6233e0f41d4a2f43c9810fbb 100644 --- a/src/nf_modules/bowtie/mapping_single.config +++ b/src/nf_modules/bowtie/mapping_single.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: mapping_fastq { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie/1.2.2/:/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" + } + } + } }