diff --git a/nextflow.config b/nextflow.config index 43a0d71..1ea7d51 100644 --- a/nextflow.config +++ b/nextflow.config @@ -35,7 +35,7 @@ params { vcfmix = 'yes' resistance_profiler = "tb-profiler" - update_tbprofiler = "true" + update_tbprofiler = "yes" // path to singularity recipes directory (needed to strip software versions in getversion) sing_dir = "${baseDir}/singularity" @@ -61,19 +61,35 @@ profiles { fixOwnership = true runOptions = "-u \$(id -u):\$(id -g)" - withLabel:getversion{ + withLabel:run_local{ executor = "local" container = null } - - withLabel:afanc_parse{ - executor = "local" - container = null + + k8s { + computeResourceType = 'Job' } + process { + executor = 'k8s' + pod = [[securityContext:[fsGroupChangePolicy:'OnRootMismatch', runAsUser:1000, runAsGroup:1000, fsGroup:1000]], [automountServiceAccountToken:false], [nodeSelector:'hub.jupyter.org/node-purpose=user'], [volumeClaim:'cephfs-shared-team', mountPath:'/shared/team'], [volumeClaim:'cephfs-shared-ro-public', mountPath:'/shared/public', readOnly:true]] + queueSize = 30 + } + k8s { + runAsUser = 1000 computeResourceType = 'Job' } + + + aws { + profile = "climb" + + client { + endpoint = 'https://s3.climb.ac.uk' + s3PathStyleAccess = true + } + } //params specific to paths on the climb system params{