test.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 sanger-tol/curationpretext -profile test,<docker/singularity> --outdir <OUTDIR>

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

process {
    resourceLimits = [
        cpus: 4,
        memory: '10.GB',
        time: '1.h'
    ]
}

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

    input           = 'https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData/assembly/draft/grTriPseu1.fa'
    reads           = ['https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData/genomic_data/pacbio/seqkitPacbio50000.fasta.gz']
    cram            = ['https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData/genomic_data/hic-arima/SUBSET-1000.cram', 'https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData/genomic_data/hic-arima/SUBSET-2000.cram']
    pre_mapped_bam  = []
    sample          = "CurationPretextTest_MIN"
    teloseq         = "TTA"
    aligner         = "bwamem2"
    all_output      = false
    skip_tracks     = "NONE"
    run_hires       = false
    run_ultra       = "no"
    split_telomere  = true
}