mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-24 06:09:54 +00:00
49 lines
2.1 KiB
Text
49 lines
2.1 KiB
Text
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
Nextflow config file for running minimal tests
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
Defines input files and everything required to run a fast and simple pipeline test.
|
|
|
|
Use as follows:
|
|
nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
|
|
|
|
----------------------------------------------------------------------------------------
|
|
*/
|
|
|
|
//
|
|
// Separate test as mOTUs database download can be flaky
|
|
//
|
|
|
|
params {
|
|
config_profile_name = 'mOTUs Test profile'
|
|
config_profile_description = 'Minimal test to check mOTUs function'
|
|
|
|
// 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/taxprofiler/samplesheet.csv'
|
|
databases = 'database_motus.csv'
|
|
perform_shortread_qc = false
|
|
perform_longread_qc = false
|
|
perform_shortread_complexityfilter = false
|
|
perform_shortread_hostremoval = false
|
|
perform_longread_hostremoval = false
|
|
perform_runmerging = false
|
|
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
|
|
run_kaiju = false
|
|
run_kraken2 = false
|
|
run_bracken = false
|
|
run_malt = false
|
|
run_metaphlan3 = false
|
|
run_centrifuge = false
|
|
run_diamond = false
|
|
run_krakenuniq = false
|
|
run_motus = true
|
|
motus_save_mgc_read_counts = false
|
|
motus_remove_ncbi_ids = false
|
|
motus_use_relative_abundance = false
|
|
run_profile_standardisation = true
|
|
}
|