diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config index d0aea31710b4a652c8bb673969395a4f49ccb29c..a85d7233c6ea571a0b0488e256aa864a4153c521 100644 --- a/src/nf_modules/rsem/indexing.config +++ b/src/nf_modules/rsem/indexing.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: index_fasta { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/rsem/1.3.0/:/usr/bin:$PATH" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" + cpus = 1 + memory = "10GB" + time = "24h" + } + } + } } diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config index 035db80fa396f1c07cef03e2b142ed0e5902bc12..58baa5c68550068751be70a555ce58f2cdd5dfeb 100644 --- a/src/nf_modules/rsem/quantification_paired.config +++ b/src/nf_modules/rsem/quantification_paired.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: mapping_fastq { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/rsem/1.3.0/:/usr/bin:$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/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config index 035db80fa396f1c07cef03e2b142ed0e5902bc12..58baa5c68550068751be70a555ce58f2cdd5dfeb 100644 --- a/src/nf_modules/rsem/quantification_single.config +++ b/src/nf_modules/rsem/quantification_single.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: mapping_fastq { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/rsem/1.3.0/:/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" + } + } + } }