diff --git a/tests/nextflow.config b/tests/nextflow.config deleted file mode 100644 index d2d63668..00000000 --- a/tests/nextflow.config +++ /dev/null @@ -1,103 +0,0 @@ -params { - // Base directory for nf-core/modules test data - modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' - - // Base directory for nf-core/fetchngs test data - pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/fetchngs/1.15.0/' - - max_cpus = 4 - max_memory = '12.GB' - time = '2.h' -} - -// Impose sensible resource limits for testing -process { - withName: BOWTIE2_PHIX_REMOVAL_ALIGN { - cpus = 1 - memory = 12.GB - time = 2.h - } - - withName: CENTRIFUGE_CENTRIFUGE { - cpus = 1 - memory = 12.GB - time = 2.h - } - - withName: BOWTIE2_ASSEMBLY_ALIGN { - cpus = 1 - memory = 12.GB - time = 2.h - } - - withName: METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS { - cpus = 1 - memory = 12.GB - time = 2.h - } - - withName: QUAST_BINS { - cpus = 1 - memory = 12.GB - time = 2.h - } - - withName: METABAT2_METABAT2 { - cpus = 1 - memory = 12.GB - time = 2.h - } -} - -// Impose same minimum Nextflow version as the pipeline for testing -manifest { - nextflowVersion = '!>=23.04.0' -} - -// Disable all Nextflow reporting options -timeline { enabled = false } -report { enabled = false } -trace { enabled = true } -dag { enabled = false } - -// Load modules test_data.config -includeConfig 'https://github.com/nf-core/modules/raw/master/tests/config/test_data.config' - - -//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -// BELOW IS ONLY FOR CJM TESTING!!! -//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -params { - config_profile_description = 'UW Hyak Pedslabs cluster profile provided by nf-core/configs.' - config_profile_contact = 'Carson J. Miller (@CarsonJM)' - config_profile_url = 'https://www.peds.uw.edu/' - // max_memory = 742.GB - // max_cpus = 40 - // max_time = 72.h - } - -process { - executor = 'slurm' - clusterOptions = { task.attempt < 4 ? ( task.attempt < 3 ? "-A stf" : "-A stf" ) : "-A pedslabs" } - - withName:'.*' { - queue = { task.attempt < 4 ? ( task.attempt < 3 ? 'cpu-g2-mem2x' : 'cpu-g2-mem2x' ) : 'compute-hugemem' } - errorStrategy = { task.attempt < 5 ? 'retry' : 'ignore' } - maxRetries = 5 - maxErrors = '-1' - } -} - -executor { - queuesize = 50 - submitRateLimit = '1 sec' -} - -singularity { - enabled = true - autoMounts = true -} - -debug { - cleanup = false -}