diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config index 22f41f8d0e42a89b7967d414ad616e5982df2526..3292c31618ded91b901a0d7da487f1e21554b9d8 100644 --- a/src/nf_modules/hisat2/indexing.config +++ b/src/nf_modules/hisat2/indexing.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: index_fasta { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/hisat2/2.1.0/:/usr/bin:$PATH" + scratch = true + stageInMode = "copy" + stageOutMode = "rsync" + executor = "sge" + clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" + cpus = 1 + memory = "10GB" + time = "24h" + } + } + } } diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config index 370f5892c4b01e600cc403abf95fa2ef07811d79..3def29115ca1faa18c91420a32eed2d7acd6ae36 100644 --- a/src/nf_modules/hisat2/mapping_paired.config +++ b/src/nf_modules/hisat2/mapping_paired.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: mapping_fastq { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/hisat2/2.1.0/:/usr/bin:$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/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config index 370f5892c4b01e600cc403abf95fa2ef07811d79..3def29115ca1faa18c91420a32eed2d7acd6ae36 100644 --- a/src/nf_modules/hisat2/mapping_single.config +++ b/src/nf_modules/hisat2/mapping_single.config @@ -33,4 +33,19 @@ profiles { } } } + ccin2p3 { + process{ + withName: mapping_fastq { + beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/hisat2/2.1.0/:/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" + } + } + } }