diff --git a/conf/pipeline/eager/custom.config b/conf/pipeline/eager/custom.config new file mode 100644 index 0000000..3543b7e --- /dev/null +++ b/conf/pipeline/eager/custom.config @@ -0,0 +1,57 @@ +/* + * ------------------------------------------------- + * Nextflow custom config file for running nf-core eager on data generated at the Francis Crick Institute + * contact: Alexandre Gilardet alexandre.gilardet@crick.ac.uk + * ------------------------------------------------- + * nextflow run nf-core/eager -profile ,crick -c custom.config + * (where is screening or production for low or high-coverage data + * respectively, or external for very high coverage) + */ + +profiles { + screening { + process { + withName:bwa { + cpus = 12 + memory = '15 GB' + time = '6h' + } + } + } + production { + process { + withName:adapter_removal { + time = '3d' + } + withName:fastp { + time = '8h' + } + withName:bwa { + cpus = 8 + memory = '56 GB' + time = '3d' + } + withName:samtools_filter { + time = '3d' + } + withName:dedup { + cpus = 6 + memory = '20 GB' + time = '3d' + } + withName:damageprofiler { + memory = '64 GB' + time = '3d' + errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' } + } + } + } + external { + process { + withName:samtools_filter { + cpus = 12 + memory = '72 GB' + } + } + } +}