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Taxa_profiling.nf.config
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/*
* -------------------------------------------------
* Taxa_profiling Nextflow config file
* -------------------------------------------------
*/
params {
// paths
GAGA_IDs = './GAGA_IDs.txt'
initial_assembly_dir = '/home/people/dinghe/ku_00039/people/dinghe/working_dr/metagenome_assembly/initial_assembly/metaflye/metagenome_candidate_reads'
GAGA_Bac_screen_dir = '/home/people/dinghe/ku_00039/people/dinghe/working_dr/metagenome_lgt/GAGA'
metaquast_dir = '/home/people/dinghe/ku_00039/people/dinghe/working_dr/metagenome_assembly/assembly_assessment/metaquast'
taxonomy_profile_dir = '/home/people/dinghe/ku_00039/people/dinghe/working_dr/metagenome_assembly/assembly_assessment/taxonomy_profile'
krakenDB = '/home/people/dinghe/ku_00039/people/dinghe/krakenDB/kraken_STD_21052021'
kronatools_dir = '/home/people/dinghe/github/Krona/KronaTools/bin'
}
process {
withLabel: 'single_core' {
cpus = 1
memory = '4 GB'
time = '1h'
}
withLabel: 'multi_core' {
cpus = 40
memory = '180 GB'
time = '2h'
}
}
profiles {
computerome {
process.executor = 'pbs'
process.module = 'tools'
}
stantard {
process.executor = 'local'
}
}
manifest {
name = 'kraken2 taxa profiling'
author = 'Ding He'
description = 'kraken2 taxa profiling'
mainScript = 'Taxa_profiling.nf'
nextflowVersion = '>=20.10.0'
version = '0.1'
}