diff --git a/nextflow.config b/nextflow.config index f1ae98d..065df87 100644 --- a/nextflow.config +++ b/nextflow.config @@ -104,17 +104,29 @@ profiles { } // includeConfig 'configs/container.config' } - test { includeConfig 'configs/test.config' } + test { + process.container = 'adamd3/strainseq:latest' + docker { + enabled = true + userEmulation = true + runOptions = '--pull=always' + } + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + includeConfig 'configs/test.config' + } } -// Export these variables to prevent local Python/R libraries from conflicting with those in the container +// Export these variables to prevent local Python/R libraries from +// conflicting with those in the container env { PYTHONNOUSERSITE = 1 R_PROFILE_USER = "/.Rprofile" R_ENVIRON_USER = "/.Renviron" } - // Default configuration for the processes in the pipeline process { cpus = { check_max( 1 * task.attempt, 'cpus' ) }