diff --git a/conf/base.config b/conf/base.config index 91f6b2208..edd0472d2 100644 --- a/conf/base.config +++ b/conf/base.config @@ -42,4 +42,23 @@ process { maxRetries = 2 } +} + +dag { + enabled = true + file = "${params.outdir}/pipeline_info/pipeline_dag.html" + overwrite = true +} + +trace { + enabled = true + file = "${params.outdir}/pipeline_info/pipeline_trace.txt" + fields = 'task_id,name,status,exit,realtime,%cpu,rss' + overwrite = true +} + +report { + enabled = true + file = "${params.outdir}/pipeline_info/pipeline_report.html" + overwrite = true } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index e0d77c342..8ac6c9275 100644 --- a/nextflow.config +++ b/nextflow.config @@ -78,13 +78,18 @@ params { } -docker { - enabled = true - fixOwnership = true +def getContainerOptions (executor) { + if (executor == 'docker') { + return '-u root:root -e USERID=$UID -e XDG_CACHE_HOME=tmp/quarto_cache_home -e XDG_DATA_HOME=tmp/quarto_data_home -e QUARTO_PRINT_STACK=true' + } else if (executor == 'singularity') { + return '--env USERID=$UID --env XDG_CACHE_HOME=tmp/quarto_cache_home --env XDG_DATA_HOME=tmp/quarto_data_home --env QUARTO_PRINT_STACK=true' + } else { + return '' + } } process { - containerOptions = '-u root:root -e USERID=$UID -e XDG_CACHE_HOME=tmp/quarto_cache_home -e XDG_DATA_HOME=tmp/quarto_data_home -e QUARTO_PRINT_STACK=true' + containerOptions = { getContainerOptions(workflow.containerEngine) } stageInMode = 'copy' } @@ -94,6 +99,7 @@ profiles { docker { docker.enabled = true docker.userEmulation = true + docker.fixOwnership = true singularity.enabled = false podman.enabled = false shifter.enabled = false @@ -108,7 +114,20 @@ profiles { shifter.enabled = false charliecloud.enabled = false } - + mskcc_iris { + singularity { + enabled = true + autoMounts = true + } + process { + executor = 'slurm' + queue = 'componc_cpu,componc_gpu' + } + executor { + name = 'slurm' + queueSize = 25 + } + } test { includeConfig 'conf/test.config' } } @@ -152,4 +171,5 @@ def check_max(obj, type) { return obj } } -} \ No newline at end of file +} +