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nextflow.config
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nextflow.config
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// NEXTFLOW MANIFEST
manifest {
name = 'umi-pipeline-nf'
version = '0.2.1'
description = 'Nextflow pipeline to analyze umi amplicon data'
author = 'Stephan Amstler'
homePage = 'https://github.com/AmstlerStephan/umi-pipeline-nf.git'
mainScript = 'main.nf'
nextflowVersion = '!>=22.04'
}
// DEFAULT PARAMETERS
params {
// BASIC PARAMS
help = false
version = false
debug = false
// GENERAL - Required
input = null
output = null
reference = null
reference_fai = null
bed = null
//READ FILTERING
min_read_length = 0
min_qscore = 0
// SUBSAMPLING
subsampling = false
subsampling_seed = 11
subsampling_readnumber = 100000
// VARIANT_CALLING
call_variants = false
variant_caller = null
// ADVANCED
min_reads_per_barcode = 1000
umi_errors = 2
max_dist_umi = 2
min_reads_per_cluster = 20
max_reads_per_cluster = 60
min_consensus_quality = 40
masking_strategy = "softmask"
filter_strategy_clusters = "quality"
output_format = "fastq"
write_reports = true
min_overlap = 0.95
include_secondary_reads = false
balance_strands = true
medaka_model = "r1041_e82_400bps_hac_g615"
fwd_umi = "TTTVVVVTTVVVVTTVVVVTTVVVVTTT"
rev_umi = "AAABBBBAABBBBAABBBBAABBBBAAA"
adapter_length = 200
min_length = 40
max_length = 60
minimap2_param = "-ax map-ont -k 13 --MD"
threads = (Runtime.runtime.availableProcessors() - 1)
}
// NEXTFLOW PROFILES
// Load base.config by default for all pipelines
includeConfig "${baseDir}/config/base.config"
process.container = 'quay.io/genepi/umi-pipeline-nf:v0.2.1'
profiles {
// -profile conda
conda {
process.conda = "${baseDir}/env/environment.yml"
}
// -profile docker
docker {
docker.enabled = true
}
// -profile singularity
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
}
// -profile test
test {
includeConfig "${baseDir}/config/test.config"
}
// -profile custom
custom {
includeConfig "${baseDir}/config/custom.config"
}
}