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taxprofiler/conf/test_pep.config
2022-11-24 16:55:19 +01:00

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params {
config_profile_name = 'Test PEP profile'
config_profile_description = 'Minimal test dataset to check pipeline function with PEP file as an input.'
// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'
// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_qc = true
perform_longread_qc = true
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
perform_runmerging = true
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = true
run_kraken2 = true
run_bracken = true
run_malt = true
run_metaphlan3 = true
run_centrifuge = true
run_diamond = true
run_motus = false
run_krona = true
krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
malt_save_reads = true
kraken2_save_reads = true
centrifuge_save_reads = true
diamond_save_reads = true
}
process {
withName: MALT_RUN {
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
}
withName: MEGAN_RMA2INFO {
maxForks = 1
}
}