mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 08:59:55 +00:00
45 lines
2 KiB
Text
45 lines
2 KiB
Text
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
|
|
}
|
|
}
|