diff --git a/conf/medair.config b/conf/medair.config index 183d4f6..eeda705 100644 --- a/conf/medair.config +++ b/conf/medair.config @@ -1,13 +1,13 @@ //Profile config names for nf-core/configs params { config_profile_description = 'Cluster profile for medair (local cluster of Clinical Genomics Gothenburg)' - config_profile_contact = 'Clinical Genomics, Gothenburg' - config_profile_url = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/' + config_profile_contact = 'Clinical Genomics, Gothenburg' + config_profile_url = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/' } //Nextflow parameters singularity { - enabled = true + enabled = true cacheDir = "/apps/bio/dependencies/nf-core/singularities" } @@ -15,26 +15,32 @@ profiles { wgs { process { - queue = 'wgs.q' - executor = 'sge' - penv = 'mpi' + queue = 'wgs.q' + executor = 'sge' + penv = 'mpi' process.clusterOptions = '-l excl=1' - params.max_cpus = 40 - params.max_time = 48.h - params.max_memory = 128.GB + params.max_cpus = 40 + params.max_time = 48.h + params.max_memory = 128.GB } } production { process { - queue = 'production.q' - executor = 'sge' - penv = 'mpi' + queue = 'production.q' + executor = 'sge' + penv = 'mpi' process.clusterOptions = '-l excl=1' - params.max_cpus = 40 - params.max_time = 480.h - params.max_memory = 128.GB + params.max_cpus = 40 + params.max_time = 480.h + params.max_memory = 128.GB } } } +//Specific parameter for pipelines that can use Sentieon (e.g. nf-core/sarek, nf-core/raredisease) +process { + withLabel:'sentieon' { + container = "/apps/bio/singularities/sentieon-211204-peta.simg" + } +}