diff --git a/nextflow.config b/nextflow.config index c31d793..bff7f39 100644 --- a/nextflow.config +++ b/nextflow.config @@ -46,14 +46,22 @@ profiles { } conda { conda.enabled = true + singularity.enabled = false params.enable_conda = true conda.createTimeout = "120 min" } mamba { conda.enabled = true + conda.useMamba = true + singularity.enabled = false params.enable_conda = true conda.createTimeout = "120 min" - conda.useMamba = true + } + singularity { + singularity.enabled = true + singularity.autoMounts = true + conda.enabled = false + params.enable_conda = false } test { includeConfig 'conf/test.config' @@ -70,6 +78,11 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set default registry for Singularity independent of -profile +// Will not be used unless Singularity is enabled +// Set to your registry if you have a mirror of containers +singularity.registry = 'quay.io' + def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true