I'm running

raredisease

on a cluster. I successfully ran it with the basic test configuration (automatic data download) and then locally with downloaded data files, a

params

file, and a

sample_sheet

. However, the pipeline gets stuck when I try to run it with full data (76GB forward and reverse files). I'm wondering if this is due to a lack of GPU access, and if the

raredisease

pipeline supports GPU acceleration.

Hi @Ali Hassan! We routinely run samples of that size on our cluster so I don't think size is an issue. Can you share your configuration files? And also make sure that raredisease isn't using the test profile somehow to set resources. That could be one reason why it is stuck. And about gpu access, pipeline as a whole doesn't need it, but there are tools in the pipeline like deepvariant that can use gpu acceleration if they are available. You might have to make some changes in the configuration to get it to work though.

Hi @Ram Thank you so much for the reply. Yes I was using the test profile, and a custom config along with it. I think that is the problem as well. I have send you the config files in the DM. BTW how long it usually takes for the pipeline to finish one sample?

On our local cluster it takes anywhere between 15-20hrs for a sample with approx 30x coverage.

Would it be okay if I copy and paste these paramenters from the test profile to my nextflow.config file?

params {
    config_profile_name             = 'Test profile - default'
    config_profile_description      = 'Minimal test dataset to check pipeline function'

    igenomes_ignore                 = true
    mito_name                       = 'MT'
    pipelines_testdata_base_path    = '<https://raw.githubusercontent.com/nf-core/test-datasets/raredisease>'

    skip_tools                      = 'fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits'
    skip_subworkflows               = "mt_annotation,mt_subsample,me_calling,me_annotation,sv_annotation"

    input                           = params.pipelines_testdata_base_path + '/testdata/samplesheet_fq_spring.csv'
    fasta                           = params.pipelines_testdata_base_path + '/reference/reference.fasta'
    fai                             = params.pipelines_testdata_base_path + '/reference/reference.fasta.fai'
    genome                          = 'GRCh37'
    gnomad_af                       = params.pipelines_testdata_base_path + '/reference/gnomad_reformated.tab.gz'
    intervals_wgs                   = params.pipelines_testdata_base_path + '/reference/target_wgs.interval_list'
    intervals_y                     = params.pipelines_testdata_base_path + '/reference/targetY.interval_list'
    known_dbsnp                     = params.pipelines_testdata_base_path + '/reference/dbsnp_-138-.vcf.gz'
    mobile_element_references       = params.pipelines_testdata_base_path + '/reference/mobile_element_references.tsv'
    mobile_element_svdb_annotations = params.pipelines_testdata_base_path + '/reference/svdb_querydb_files.csv'
    reduced_penetrance              = params.pipelines_testdata_base_path + '/reference/reduced_penetrance.tsv'
    score_config_mt                 = params.pipelines_testdata_base_path + '/reference/rank_model_snv.ini'
    score_config_snv                = params.pipelines_testdata_base_path + '/reference/rank_model_snv.ini'
    score_config_sv                 = params.pipelines_testdata_base_path + '/reference/rank_model_sv.ini'
    svdb_query_dbs                  = params.pipelines_testdata_base_path + '/reference/svdb_querydb_files.csv'
    target_bed                      = params.pipelines_testdata_base_path + '/reference/target.bed'
    variant_catalog                 = params.pipelines_testdata_base_path + '/reference/variant_catalog.json'
    vcfanno_lua                     = params.pipelines_testdata_base_path + '/reference/vcfanno_functions.lua'
    vcfanno_resources               = params.pipelines_testdata_base_path + '/reference/vcfanno_resources.txt'
    vcfanno_toml                    = params.pipelines_testdata_base_path + '/reference/vcfanno_config.toml'
    variant_consequences_snv        = params.pipelines_testdata_base_path + '/reference/variant_consequences_v2.txt'
    variant_consequences_sv         = params.pipelines_testdata_base_path + '/reference/variant_consequences_v2.txt'
    vep_cache                       = params.pipelines_testdata_base_path + '/reference/vep_cache_and_plugins.tar.gz'
    vep_filters                     = params.pipelines_testdata_base_path + '/reference/hgnc.txt'
    vep_cache_version               = 107
    vep_plugin_files                = params.pipelines_testdata_base_path + '/reference/vep_files.csv'

}