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nextflow.config
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nextflow.config
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// Parameters
params {
// Output Directory
outdir = './results'
// cache for conda
cache = ''
// Nanopore reads
nanopore = false
// Illumina reads
illumina = false
// References - You will need to link your own human reference up with `--human_ref <reference>`
human_ref = '/cvmfs/data.galaxyproject.org/byhand/hg38/seq/hg38.fa'
cov2019_ref = "$baseDir/data/nCoV-2019.reference.fasta"
// Extras
tracedir = '${params.outdir}/pipeline_info'
}
// Load Resources
includeConfig 'conf/resources.config'
if ( params.nanopore ){
includeConfig 'conf/nanopore.config'
}
if ( params.illumina ){
includeConfig 'conf/illumina.config'
}
profiles {
conda {
// Time out time
conda.createTimeout = '1 h'
// Create base environment
process.conda = "$baseDir/environments/base.yml"
if (params.cache) {
conda.cacheDir = params.cache
}
}
nml {
includeConfig 'conf/custom/nml.config'
}
// Add more custom profiles here
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = false
file = '${params.tracedir}/execution_timeline.html'
}
report {
enabled = false
file = '${params.tracedir}/execution_report.html'
}
trace {
enabled = false
file = '${params.tracedir}/execution_trace.txt'
}
dag {
enabled = false
file = '${params.tracedir}/pipeline_dag.svg'
}
manifest {
author = 'Darian Hole'
description = 'Removal of human reads from SARS-CoV-2 fastq and fast 5 files'
mainScript = 'main.nf'
nextflowVersion = '>=20.01.0'
version = '0.1.0'
}