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nextflow.config
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nextflow.config
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manifest {
author = 'Dan Fornika'
name = 'BCCDC-PHL/plasmid-screen'
description = 'Plasmid Screen'
mainScript = 'main.nf'
nextflowVersion = '>=20.01.0'
version = '0.2.3'
}
params {
outdir = './results'
assembly_exts = ['*.fa', '*.fasta', '*.fna']
assembly_search_path = makeAssemblySearchPath( assembly_exts )
pre_assembled = false
illumina_suffixes = ['*_R{1,2}_001', '*_R{1,2}', '*_{1,2}' ]
fastq_exts = ['.fastq.gz', '.fq.gz', '.fastq', '.fq']
fastq_search_path = makeFastqSearchPath( illumina_suffixes, fastq_exts )
fastq_input = 'NO_FILE'
assembly_input = 'NO_FILE'
samplesheet_input = 'NO_FILE'
mob_filter_db = '/data/ref_databases/mob-suite/chromosomes/2019-11-NCBI-Enterobacteriacea-Chromosomes/2019-11-NCBI-Enterobacteriacea-Chromosomes.fasta'
blast_percent_identity = 98
blast_min_length = 100
mashthreshold = 0.996
min_plasmid_coverage_depth = 10
min_plasmid_coverage_breadth = 95
collect_outputs = false
collected_outputs_prefix = 'collected'
pipeline_short_name = parsePipelineName(manifest.toMap().get('name'))
pipeline_minor_version = parseMinorVersion(manifest.toMap().get('version'))
}
def makeAssemblySearchPath(assembly_exts) {
def assembly_search_path = []
for (ext in assembly_exts) {
assembly_search_path.add(params.assembly_input.toString() + '/' + ext.toString())
assembly_search_path.add(params.assembly_input.toString() + '/**/' + ext.toString())
}
return assembly_search_path
}
def makeFastqSearchPath(illumina_suffixes, fastq_exts) {
def fastq_search_path = []
for (suffix in illumina_suffixes){
for (ext in fastq_exts) {
fastq_search_path.add(params.fastq_input.toString() + '/' + suffix.toString() + ext.toString())
}
}
return fastq_search_path
}
def parseMinorVersion(version) {
minor_version = version.split('\\.')[0..1].join('.')
return minor_version
}
def parsePipelineName(name) {
short_name = name.split('/')[1]
return short_name
}
profiles {
conda {
conda.enabled = true
process.conda = "$baseDir/environments/environment.yml"
if (params.cache){
conda.cacheDir = params.cache
}
}
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
process {
withName: unicycler {
cpus = 16
}
withName: quast {
cpus = 4
}
withName: mash_screen {
cpus = 4
}
withName: mob_recon {
cpus = 4
}
withName: align_reads_to_reference_plasmid {
cpus = 4
}
withName: call_snps {
conda = "$baseDir/environments/freebayes.yml"
}
}