test_full_somatic.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Nextflow config file for running full-size tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Defines input files and everything required to run a full size pipeline test.

    Use as follows:
        nextflow run nf-core/sarek -profile test_full_somatic,<docker/singularity> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/

params {
    config_profile_name        = 'Full test profile for somatic VC'
    config_profile_description = 'Full test dataset to check somatic VC pipeline function'

    // Input data for full size test
    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/HCC1395_WXS_somatic_full_test.csv'

    // Other params
    tools = 'strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep'
    split_fastq = 20000000
    intervals   = 's3://nf-core-awsmegatests/sarek/input/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
    wes         = true
}