mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-24 09:09:56 +00:00
23 lines
847 B
Text
23 lines
847 B
Text
/*
|
|
* -------------------------------------------------
|
|
* Nextflow config file for GIS (Aquila)
|
|
* -------------------------------------------------
|
|
* Defines reference genomes, using iGenome paths
|
|
* Imported under the default 'standard' Nextflow
|
|
* profile in nextflow.config
|
|
*/
|
|
|
|
process {
|
|
executor = 'sge'
|
|
clusterOptions = { "-l mem_free=" + task.memory.toString().replaceAll(/[\sB]/,'') }
|
|
penv = 'OpenMP'
|
|
errorStrategy = { task.attempt < 2 ? 'retry' : 'finish' }
|
|
// auto translate container name into conda environment name
|
|
beforeScript = { 'source /mnt/projects/rpd/rc/init.2017-04; module load miniconda3; set +u; source activate nfcore-rnaseq-1.0dev; set -u;' }
|
|
}
|
|
params {
|
|
saveReference = true
|
|
// illumina iGenomes reference file paths on GIS Aquila
|
|
igenomes_base = '/mnt/projects/rpd/genomes.testing/S3_igenomes/'
|
|
}
|
|
|