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nextflow.config
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/*
* -------------------------------------------------
* nf-core/eager Nextflow config file
* -------------------------------------------------
* Default config options for all environments.
*/
// Global default params, used in configs
params {
// Workflow flags
genome = false
single_end = false
outdir = './results'
publish_dir_mode = 'copy'
// aws
awsqueue = ''
awsregion = 'eu-west-1'
awscli = ''
//Pipeline options
//Input reads
input = null
udg_type = 'none'
single_stranded = false
single_end = false
colour_chemistry = 4
bam = false
// Optional input information
snpcapture_bed = ''
run_convertinputbam = false
//Input reference
fasta = ''
bwa_index = ''
bt2_index = ''
fasta_index = ''
seq_dict = ''
large_ref = false
save_reference = false
saveTrimmed = true
saveAlignedIntermediates = false
//Skipping parts of the pipeline for impatient users
skip_fastqc = false
skip_adapterremoval = false
skip_preseq = false
skip_deduplication = false
skip_damage_calculation = false
skip_qualimap = false
//More defaults
complexity_filter_poly_g = false
complexity_filter_poly_g_min = 10
//Read clipping and merging parameters
clip_forward_adaptor = 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
clip_reverse_adaptor = 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
clip_readlength = 30
clip_min_read_quality = 20
min_adap_overlap = 1
skip_collapse = false
skip_trim = false
preserve5p = false
mergedonly = false
//Mapping algorithm
mapper = 'bwaaln'
bwaalnn = 0.04
bwaalnk = 2
bwaalnl = 1024 // From Schubert et al. 2012 (10.1186/1471-2164-13-178)
circularextension = 500
circulartarget = 'MT'
circularfilter = false
bt2_alignmode = 'local' // from Cahill 2018 (10.1093/molbev/msy018) and, Poullet and Orlando (10.3389/fevo.2020.00105)
bt2_sensitivity = 'sensitive' // from Poullet and Orlando (10.3389/fevo.2020.00105)
bt2n = 0 // Do not set Cahill 2018 recommendation of 1 here, so not to 'hide' overriding bowtie2 presets
bt2l = 0
bt2_trim5 = 0
bt2_trim3 = 0
//Mapped read removal from input FASTQ
hostremoval_input_fastq = false
hostremoval_mode = 'remove'
//BAM Filtering steps (default = discard unmapped reads)
run_bam_filtering = false
bam_mapping_quality_threshold = 0
bam_filter_minreadlength = 0
bam_unmapped_type = 'discard'
//DeDuplication settings
dedupper = 'markduplicates'
dedup_all_merged = false
//Preseq settings
preseq_step_size = 1000
//DamageProfiler settings
damageprofiler_length = 100
damageprofiler_threshold = 15
damageprofiler_yaxis = 0.30
//PMDTools settings
run_pmdtools = false
pmdtools_range = 10
pmdtools_threshold = 3
pmdtools_reference_mask = ''
pmdtools_max_reads = 10000
// mapDamage
run_mapdamage_rescaling = false
params.rescale_length_5p = 12
params.rescale_length_3p = 12
//Bedtools settings
run_bedtools_coverage = false
anno_file = ''
//bamUtils trimbam settings
run_trim_bam = false
bamutils_clip_half_udg_left = 1
bamutils_clip_half_udg_right = 1
bamutils_clip_none_udg_left = 1
bamutils_clip_none_udg_right = 1
bamutils_softclip = false
//Genotyping options
run_genotyping = false
genotyping_tool = ''
genotyping_source = 'raw'
// gatk options
gatk_call_conf = 30
gatk_ploidy = 2
gatk_downsample = 250
gatk_dbsnp = ''
gatk_hc_out_mode = 'EMIT_VARIANTS_ONLY'
gatk_hc_emitrefconf = 'GVCF'
gatk_ug_genotype_model = 'SNP'
gatk_ug_out_mode = 'EMIT_VARIANTS_ONLY'
gatk_ug_keep_realign_bam = false
gatk_ug_defaultbasequalities = ''
// freebayes options
freebayes_C = 1
freebayes_g = 0
freebayes_p = 2
// Sequencetools pileupCaller
pileupcaller_snpfile = ''
pileupcaller_bedfile = ''
pileupcaller_method = 'randomHaploid'
pileupcaller_transitions_mode = 'AllSites'
// ANGSD Genotype Likelihoods
angsd_glmodel = 'samtools'
angsd_glformat = 'binary'
angsd_createfasta = false
angsd_fastamethod = 'random'
//Consensus sequence generation
run_vcf2genome = false
vcf2genome_outfile = ''
vcf2genome_header = ''
vcf2genome_minc = 5
vcf2genome_minq = 30
vcf2genome_minfreq = 0.8
//MultiVCFAnalyzer Options
run_multivcfanalyzer = false
write_allele_frequencies = false
min_genotype_quality = 30
min_base_coverage = 5
min_allele_freq_hom = 0.9
min_allele_freq_het = 0.9
additional_vcf_files = ''
reference_gff_annotations = 'NA'
reference_gff_exclude = 'NA'
snp_eff_results = 'NA'
//mtnucratio
run_mtnucratio = false
mtnucratio_header = 'MT'
//Sex.DetERRmine settings
run_sexdeterrmine = false
sexdeterrmine_bedfile = ''
//Nuclear contamination based on chromosome X heterozygosity.
run_nuclear_contamination = false
contamination_chrom_name = 'X' // Default to using hs37d5 name
// taxonomic classifier
run_metagenomic_screening = false
metagenomic_complexity_filter = false
metagenomic_complexity_entropy = 0.3
metagenomic_tool = ''
database = ''
metagenomic_min_support_reads = 1
percent_identity = 85
malt_mode = 'BlastN'
malt_alignment_mode = 'SemiGlobal'
malt_top_percent = 1
malt_min_support_mode = 'percent'
malt_min_support_percent = 0.01
malt_max_queries = 100
malt_memory_mode = 'load'
malt_sam_output = false
// maltextract - only including number
// parameters if default documented or duplicate of MALT
run_maltextract = false
maltextract_taxon_list = ''
maltextract_ncbifiles = ''
maltextract_filter = 'def_anc'
maltextract_toppercent = 0.01
maltextract_destackingoff = false
maltextract_downsamplingoff = false
maltextract_duplicateremovaloff = false
maltextract_matches = false
maltextract_megansummary = false
maltextract_percentidentity = 85.0
maltextract_topalignment = false
// Boilerplate options
name = false
multiqc_config = false
email = false
email_on_fail = false
max_multiqc_email_size = 25.MB
plaintext_email = false
monochrome_logs = false
help = false
igenomes_base = 's3://ngi-igenomes/igenomes/'
tracedir = "${params.outdir}/pipeline_info"
igenomes_ignore = false
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = false
config_profile_description = false
config_profile_contact = false
config_profile_url = false
// Defaults only, expecting to be overwritten
max_memory = 128.GB
max_cpus = 16
max_time = 240.h
}
// Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev
process.container = 'nfcore/eager:2.3.1'
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/eager custom profiles from different institutions
try {
includeConfig "${params.custom_config_base}/pipeline/eager.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/eager profiles: ${params.custom_config_base}/pipeline/eager.config")
}
profiles {
conda { process.conda = "$projectDir/environment.yml" }
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
// Avoid this error:
// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
// Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
// once this is established and works well, nextflow might implement this behavior as new default.
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
podman {
podman.enabled = true
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_bam { includeConfig 'conf/test_bam.config'}
test_fna { includeConfig 'conf/test_fna.config'}
test_humanbam { includeConfig 'conf/test_humanbam.config' }
test_pretrim { includeConfig 'conf/test_pretrim.config' }
test_kraken { includeConfig 'conf/test_kraken.config' }
test_tsv { includeConfig 'conf/test_tsv.config'}
test_tsv_bam { includeConfig 'conf/test_tsv_bam.config'}
test_tsv_fna { includeConfig 'conf/test_tsv_fna.config'}
test_tsv_humanbam { includeConfig 'conf/test_tsv_humanbam.config' }
test_tsv_pretrim { includeConfig 'conf/test_tsv_pretrim.config' }
test_tsv_kraken { includeConfig 'conf/test_tsv_kraken.config' }
test_tsv_complex { includeConfig 'conf/test_tsv_complex.config' }
test_stresstest_human { includeConfig 'conf/test_stresstest_human.config' }
benchmarking_human { includeConfig 'conf/benchmarking_human.config' }
benchmarking_vikingfish { includeConfig 'conf/benchmarking_vikingfish.config' }
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = true
file = "${params.tracedir}/execution_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag.svg"
}
manifest {
name = 'nf-core/eager'
author = 'The nf-core/eager community'
homePage = 'https://github.com/nf-core/eager'
description = 'A fully reproducible and state-of-the-art ancient DNA analysis pipeline'
mainScript = 'main.nf'
nextflowVersion = '!>=20.04.0'
version = '2.3.1'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}