diff --git a/src/nf_modules/Kallisto/indexing.config b/src/nf_modules/Kallisto/indexing.config index 94c14cd210981318ff555888b96f3c43796a9c66..0e8b5632af47704d2724db21d193860dc2286a91 100644 --- a/src/nf_modules/Kallisto/indexing.config +++ b/src/nf_modules/Kallisto/indexing.config @@ -3,24 +3,25 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - $index_fasta { + withName: index_fasta { container = "kallisto:0.44.0" } } } sge { process{ - $index_fasta { - beforeScript = "module purge; module load Kallisto/0.44.0" + withName: index_fasta { + beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" + module = "Kallisto/0.44.0" executor = "sge" - cpus = 1 - memory = "5GB" - time = "6h" - queueSize = 1000 - pollInterval = '60sec' - queue = 'h6-E5-2667v4deb128' - penv = 'openmp8' + cpus = 16 + memory = "30GB" + time = "24h" + queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' + penv = 'openmp16' } } } } + + diff --git a/src/nf_modules/Kallisto/mapping_paired.config b/src/nf_modules/Kallisto/mapping_paired.config index de674527ae0735b3797dc69fe7ae90b6557e1fa1..5a6102d99b7bb1d179eedee6f9a53cbd126517b3 100644 --- a/src/nf_modules/Kallisto/mapping_paired.config +++ b/src/nf_modules/Kallisto/mapping_paired.config @@ -3,24 +3,25 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - $mapping_fastq { + withName: mapping_fastq { container = "kallisto:0.44.0" } } } sge { process{ - $mapping_fastq { - beforeScript = "module purge; module load Kallisto/0.44.0" + withName: mapping_fastq { + beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" + module = "Kallisto/0.44.0" executor = "sge" - cpus = 4 - memory = "5GB" - time = "6h" - queueSize = 1000 - pollInterval = '60sec' - queue = 'h6-E5-2667v4deb128' - penv = 'openmp8' + cpus = 16 + memory = "30GB" + time = "24h" + queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' + penv = 'openmp16' } } } } + + diff --git a/src/nf_modules/Kallisto/mapping_single.config b/src/nf_modules/Kallisto/mapping_single.config index de674527ae0735b3797dc69fe7ae90b6557e1fa1..5a6102d99b7bb1d179eedee6f9a53cbd126517b3 100644 --- a/src/nf_modules/Kallisto/mapping_single.config +++ b/src/nf_modules/Kallisto/mapping_single.config @@ -3,24 +3,25 @@ profiles { docker.temp = 'auto' docker.enabled = true process { - $mapping_fastq { + withName: mapping_fastq { container = "kallisto:0.44.0" } } } sge { process{ - $mapping_fastq { - beforeScript = "module purge; module load Kallisto/0.44.0" + withName: mapping_fastq { + beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" + module = "Kallisto/0.44.0" executor = "sge" - cpus = 4 - memory = "5GB" - time = "6h" - queueSize = 1000 - pollInterval = '60sec' - queue = 'h6-E5-2667v4deb128' - penv = 'openmp8' + cpus = 16 + memory = "30GB" + time = "24h" + queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F' + penv = 'openmp16' } } } } + +