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nextflow.config
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nextflow.config
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manifest {
/* Homepage of project */
homePage = 'https://github.com/meglab-metagenomics/amrplusplus_v2'
/* Description of project */
description = 'AmrPlusPlus: A bioinformatic pipeline for characterizing the resistome with the MEGARes database and the microbiome using Kraken.'
/* Main pipeline script */
mainScript = 'main_AmrPlusPlus_v2.nf'
/* Default repository branch */
defaultBranch = 'master'
}
params {
/* Location of forward and reverse read pairs */
reads = "data/raw/*_R{1,2}.fastq.gz"
/* Location of adapter sequences */
adapters = "data/adapters/nextera.fa"
/* Location of host genome index files */
host_index = ""
/* Location of host genome */
host = "data/host/chr21.fasta.gz"
/* Kraken database location, default is "none" */
kraken_db = "minikraken2_v2_8GB_201904_UPDATE"
/* Location of amr index files */
amr_index = ""
/* Location of antimicrobial resistance (MEGARes) database */
amr = "data/amr/megares_modified_database_v2.00.fasta"
/* Location of amr annotation file */
annotation = "data/amr/megares_modified_annotations_v2.00.csv"
/* Location of SNP confirmation script */
snp_confirmation = "bin/snp_confirmation.py"
/* Output directory */
output = "test_results"
/* Number of threads */
threads = 10
smem_threads = 12
/* Trimmomatic trimming parameters */
leading = 3
trailing = 3
slidingwindow = "4:15"
minlen = 36
/* Resistome threshold */
threshold = 80
/* Starting rarefaction level */
min = 5
/* Ending rarefaction level */
max = 100
/* Number of levels to skip */
skip = 5
/* Number of iterations to sample at */
samples = 1
/* Display help message */
help = false
}
/* These files correspond to configuration files that can be edited to best suit your computing environment. */
profiles {
local {
includeConfig "config/local.config"
}
MEG_AMI {
includeConfig "config/MEG_AMI.config"
}
local_angus {
includeConfig "config/local_angus.config"
}
local_MSI {
includeConfig "config/local_MSI.config"
}
singularity_slurm {
process.executor = 'slurm'
includeConfig "config/singularity_slurm.config"
process.container = 'shub://meglab-metagenomics/amrplusplus_v2'
}
singularity {
includeConfig "config/singularity.config"
process.container = 'shub://meglab-metagenomics/amrplusplus_v2'
}
}