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nextflow.config
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nextflow.config
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manifest {
author = 'Dan Fornika <[email protected]>'
name = 'BCCDC-PHL/amplicon-consensus'
description = 'Amplicon-based consensus sequence pipeline'
mainScript = 'main.nf'
nextflowVersion = '>=20.01.0'
version = '0.1.0'
}
params {
profile = false
cache = ''
illumina_suffixes = ['*_R{1,2}_001', '*_R{1,2}', '*_{1,2}' ]
nanopore_suffixes = ['*_RL']
fastq_exts = ['.fastq.gz', '.fq.gz', '.fastq', '.fq']
fastq_search_path = makeFastqSearchPath( params.fastq_input, illumina_suffixes, fastq_exts )
fastq_input = 'NO_FILE'
samplesheet_input = 'NO_FILE'
ref = 'NO_FILE'
bed = 'NO_FILE'
align_untrimmed_reads = false
unambiguous_allele_freq_threshold = 0.75
ambiguous_allele_freq_threshold = 0.25
min_qual_for_variant_calling = 20
min_depth = 10
max_depth = 0
qualimap_memory = '4G'
qualimap_coverage_histogram_limit = 100
coverage_plot_y_limit = 2000
coverage_plot_log_scale = false
coverage_plot_width_inches_per_mb = 400
coverage_plot_height_inches_per_chrom = 6
coverage_plot_window_size = 50
outdir = 'results'
collect_outputs = false
collected_outputs_prefix = 'collected'
pipeline_short_name = parsePipelineName(manifest.toMap().get('name'))
pipeline_minor_version = parseMinorVersion(manifest.toMap().get('version'))
}
def makeFastqSearchPath ( base_path, fastq_suffixes, fastq_exts ) {
def fastq_search_path = []
for (suffix in fastq_suffixes){
for (ext in fastq_exts) {
fastq_search_path.add(base_path.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 = "$baseDir/environments/environment.yml"
if (params.cache){
conda.cacheDir = params.cache
}
}
}
process {
withName: bwa_mem {
cpus = 24
}
withName: qualimap_bamqc {
cpus = 16
memory = '36G'
}
withName: plot_coverage {
conda = "$baseDir/environments/plot_coverage.yml"
}
withName: plot_amplicon_coverage {
conda = "$baseDir/environments/plot_coverage.yml"
}
}