curationpretext/conf/test_full.config at bfdaaf07463d59a0965184fed713770e796025d7 · sanger-tol/curationpretext · GitHub

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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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_full,<docker/singularity> --outdir <OUTDIR>

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

cleanup = true

executor.cpus = 50
executor.memory = 50.GB
executor.time = 1.h

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

    // Input data for full size test
    // Limit resources so that this can run on GitHub Actions

    sample      = "testing"
    input       = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValTinyData/assembly/draft/grTriPseu1.fa"
    longread    = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValTinyData/genomic_data/pacbio/"
    cram        = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValTinyData/genomic_data/hic-arima/"
    sample      = "CurationPretextTest"
    teloseq     = "TTAGGG"
    aligner     = "bwamem2"
}