diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config index 403d94263b80aecdf743250d93d0bc68f63554da..84c2a2f4e4af76f2ddaaf85581a088d1cbf2f5ff 100644 --- a/src/nf_modules/kallisto/indexing.config +++ b/src/nf_modules/kallisto/indexing.config @@ -42,11 +42,9 @@ profiles { stageOutMode = "rsync" executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" - cpus = 4 - memory = "8GB" + cpus = 1 + memory = "10GB" time = "24h" - queue = 'mc_huge' - penv = 'multicores' } } } diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config index a8c439b950c294cc3ebad6ed0855e5dfd697f1d6..48ee3405404c76f2f94f0f9a9f5d25ece351cd4b 100644 --- a/src/nf_modules/kallisto/mapping_paired.config +++ b/src/nf_modules/kallisto/mapping_paired.config @@ -33,6 +33,21 @@ profiles { } } } + ccin2p3 { + process{ + withName: mapping_fastq { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/usr/bin:$PATH" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" + cpus = 1 + memory = "10GB" + time = "24h" + } + } + } } diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config index a8c439b950c294cc3ebad6ed0855e5dfd697f1d6..48ee3405404c76f2f94f0f9a9f5d25ece351cd4b 100644 --- a/src/nf_modules/kallisto/mapping_single.config +++ b/src/nf_modules/kallisto/mapping_single.config @@ -33,6 +33,21 @@ profiles { } } } + ccin2p3 { + process{ + withName: mapping_fastq { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/usr/bin:$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" + } + } + } }