/*

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Nextflow config file for running minimal tests

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Runs input data but skipping all possible steps to allow for a fast testing

profile for input checks etc.

Use as follows:

nextflow run nf-core/mag -profile test_minimal,<docker/singularity> --outdir <OUTDIR>

----------------------------------------------------------------------------------------

*/

// Limit resources so that this can run on GitHub Actions

process {

resourceLimits = [

cpus: 4,

memory: '15.GB',

time: '1.h',

]

}

params {

config_profile_name = 'Test nothing profile'

config_profile_description = 'Minimal test dataset to check pipeline function'

// Input data

input = params.pipelines_testdata_base_path + 'mag/samplesheets/samplesheet.v4.csv'

skip_clipping = true

skip_adapter_trimming = true

skip_longread_filtering = true

skip_spades = true

skip_spadeshybrid = true

skip_megahit = true

skip_metamdbg = false

skip_flye = false

skip_quast = true

skip_prodigal = true

skip_binning = true

skip_metabat2 = true

skip_maxbin2 = true

skip_concoct = true

skip_prokka = true

skip_binqc = true

skip_gtdbtk = true

skip_ancient_damagecorrection = true

gtdbtk_min_completeness = 0.01

skip_metaeuk = true

}