diff --git a/src/RNAseq.config b/src/RNAseq.config index e35b49a2cfb6a7b44dbe8bd5fb69fcdefd33d25d..c64610538b89ea9b4c2252f94d09a68e091584bf 100644 --- a/src/RNAseq.config +++ b/src/RNAseq.config @@ -77,4 +77,44 @@ profiles { } } } -} \ No newline at end of file +} +profiles { + docker { + docker.temp = 'auto' + docker.enabled = true + process { + $index_fasta { + container = "kallisto:0.43.1" + } + $mapping_fastq { + container = "kallisto:0.43.1" + } + } + } + sge { + process{ + $index_fasta { + beforeScript = "module purge; module load Kallisto/0.43.1" + executor = "sge" + cpus = 1 + memory = "5GB" + time = "6h" + queueSize = 1000 + pollInterval = '60sec' + queue = 'h6-E5-2667v4deb128' + penv = 'openmp8' + } + $mapping_fastq { + beforeScript = "module purge; module load Kallisto/0.43.1" + executor = "sge" + cpus = 4 + memory = "5GB" + time = "6h" + queueSize = 1000 + pollInterval = '60sec' + queue = 'h6-E5-2667v4deb128' + penv = 'openmp8' + } + } + } +}