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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/raredisease Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Required options
input = null
// References
genome = 'GRCh38'
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = false
local_genomes = null
save_reference = false
mito_name = 'chrM'
// Main options
analysis_type = 'wgs'
bwa_as_fallback = false
bait_padding = 100
extract_alignments = false
restrict_to_contigs = null
run_mt_for_wes = false
run_rtgvcfeval = false
save_mapped_as_cram = false
scatter_count = 20
skip_fastp = false
skip_gens = true
skip_germlinecnvcaller = false
skip_peddy = false
skip_me_calling = false
skip_me_annotation = false
skip_mt_annotation = false
skip_repeat_annotation = false
skip_repeat_calling = false
skip_smncopynumbercaller = false
skip_snv_annotation = false
skip_snv_calling = false
skip_sv_annotation = false
skip_sv_calling = false
skip_mt_subsample = false
skip_vcf2cytosure = true
skip_vep_filter = false
cadd_resources = null
platform = 'illumina'
// reference file options
fasta = null
fai = null
bwa = null
bwamem2 = null
bwameme = null
call_interval = null
cadd_resources = null
gcnvcaller_model = null
gens_interval_list = null
gens_pon_female = null
gens_pon_male = null
gens_gnomad_pos = null
gnomad_af = null
gnomad_af_idx = null
intervals_wgs = null
intervals_y = null
known_dbsnp = null
known_dbsnp_tbi = null
mobile_element_references = null
mobile_element_svdb_annotations = null
ml_model = null
mt_fasta = null
par_bed = null
ploidy_model = null
reduced_penetrance = null
readcount_intervals = null
rtg_truthvcfs = null
sample_id_map = null
sequence_dictionary = null
score_config_mt = null
score_config_snv = null
score_config_sv = null
sdf = null
svdb_query_bedpedbs = null
svdb_query_dbs = null
target_bed = null
variant_catalog = null
variant_consequences_snv = null
variant_consequences_sv = null
vep_filters = null
vep_filters_scout_fmt = null
vcf2cytosure_blacklist = null
vcfanno_extra_resources = null
vcfanno_resources = null
vcfanno_toml = null
vcfanno_lua = null
vep_cache = null
vep_plugin_files = null
// Bam_qc
ngsbits_samplegender_method = 'xy'
// Alignment
aligner = 'bwamem2'
mt_aligner = 'bwamem2'
mbuffer_mem = 3072
samtools_sort_threads = 4
min_trimmed_length = 40
mt_subsample_rd = 150
mt_subsample_seed = 30
rmdup = false
// Variant calling
cnvnator_binsize = 1000
variant_caller = 'deepvariant'
// variant annotation
vep_cache_version = 112
// sentieon Defaults
ml_model = ''
// Dnascope SNV calling
sentieon_dnascope_pcr_indel_model = 'CONSERVATIVE'
variant_type = 'snp,indel'
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
help_full = false
show_hidden = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Schema validation default options
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.channels = ['conda-forge', 'bioconda']
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
wave {
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
wave.enabled = true
wave.freeze = true
wave.strategy = 'conda,container'
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
process {
resourceLimits = [
memory: 8.GB,
cpus : 4,
time : 1.h
]
}
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_one_sample { includeConfig 'conf/test_one_sample.config' }
test_sentieon { includeConfig 'conf/test_sentieon.config' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf-core/raredisease custom profiles from different institutions.
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/raredisease.config" : "/dev/null"
// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
charliecloud.registry = 'quay.io'
// Load igenomes.config if required
includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Set bash options
process.shell = [
"bash",
"-C", // No clobber - prevent output redirection from overwriting files.
"-e", // Exit if a tool returns a non-zero status/exit code
"-u", // Treat unset variables and parameters as an error
"-o pipefail" // Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
]
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}
manifest {
name = 'nf-core/raredisease'
author = """Clinical Genomics Stockholm""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
contributors = [
[
name: 'Ramprasad Neethiraj',
affiliation: 'School of Engineering sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden',
email: '[email protected]',
github: 'https://github.com/ramprasadn',
contribution: ['author', 'maintainer'],
orcid: 'https://orcid.org/0000-0001-7313-3734'
],
[
name: 'Anders Jemt',
affiliation: 'Genomics Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden',
email: '[email protected]',
github: 'https://github.com/jemten',
contribution: ['author', 'maintainer'],
orcid: 'https://orcid.org/0000-0002-2219-0197'
],
[
name: 'Mei Wu',
github: 'https://github.com/projectoriented',
contribution: ['contributor']
],
[
name: 'Lucía Peña-Pérez',
affiliation: 'Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden',
email: '[email protected]',
github: 'https://github.com/Lucpen',
contribution: ['contributor'],
orcid: 'https://orcid.org/0000-0002-5044-7754'
],
[
name: 'Peter Pruisscher',
affiliation: 'Genomics Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden',
email: '[email protected]',
github: 'https://github.com/peterpru',
contribution: ['contributor'],
orcid: 'https://orcid.org/0000-0002-6987-5839'
],
[
name: 'Anders Sune Pedersen',
affiliation: 'Danish National Genome Center',
email: '[email protected]',
github: 'https://github.com/asp8200',
contribution: ['contributor'],
orcid: 'https://orcid.org/0009-0008-1112-841X'
],
[
name: 'Gwenna Breton',
affiliation: 'Clinical Genomics Gothenburg, Sahlgrenska University Hospital and University of Gothenburg',
email: '[email protected]',
github: 'https://github.com/Gwennid',
contribution: ['contributor'],
orcid: 'https://orcid.org/0000-0002-4100-9963'
],
[
name: 'Sima Rahimi',
affiliation: 'Clinical Genomics Lund, Lund University',
email: '[email protected]',
github: 'https://github.com/sima-r',
contribution: ['contributor']
],
[
name: 'Felix Lenner',
affiliation: 'Department of Immunology, Genetics and Pathology, Uppsala University, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden',
email: '[email protected]',
github: 'https://github.com/fellen31',
contribution: ['contributor'],
orcid: 'https://orcid.org/0000-0002-9594-0710'
],
[
name: 'Maxime U Garcia',
affiliation: 'Seqera',
email: '[email protected]',
github: 'https://github.com/maxulysse',
contribution: ['contributor'],
orcid: 'https://orcid.org/0000-0003-2827-9261'
],
[
name: 'Eva Caceres',
affiliation: 'Clinical Genomics Stockholm',
email: '[email protected]',
github: 'https://github.com/fevac',
contribution: ['contributor']
],
[
name: 'and the nf-core/raredisease team',
affiliation: 'nf-core community',
email: '',
github: 'https://github.com/nf-core',
contribution: ['contributor'],
orcid: ''
]
]
homePage = 'https://github.com/nf-core/raredisease'
description = """call and score variants from WGS/WES of rare disease patients"""
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=24.04.2'
version = '2.3.0'
doi = '10.5281/zenodo.7995798'
}
// Load DSL2 module options from config files, where each file contains the options for modules used in the eponymous subworkflow.
includeConfig 'conf/modules/raredisease.config'
includeConfig 'conf/modules/align.config'
includeConfig 'conf/modules/annotate_consequence_pli.config'
includeConfig 'conf/modules/annotate_genome_snvs.config'
includeConfig 'conf/modules/annotate_mt_snvs.config'
includeConfig 'conf/modules/annotate_structural_variants.config'
includeConfig 'conf/modules/annotate_repeat_expansions.config'
includeConfig 'conf/modules/call_repeat_expansions.config'
includeConfig 'conf/modules/call_snv.config'
includeConfig 'conf/modules/call_structural_variants.config'
includeConfig 'conf/modules/convert_mt_bam_to_fastq.config'
includeConfig 'conf/modules/generate_cytosure_files.config'
includeConfig 'conf/modules/gens.config'
includeConfig 'conf/modules/prepare_references.config'
includeConfig 'conf/modules/qc_bam.config'
includeConfig 'conf/modules/rank_variants.config'
includeConfig 'conf/modules/scatter_genome.config'
includeConfig 'conf/modules/align_MT.config'
includeConfig 'conf/modules/align_bwa_bwamem2_bwameme.config'
includeConfig 'conf/modules/align_sentieon.config'
includeConfig 'conf/modules/annotate_cadd.config'
includeConfig 'conf/modules/call_snv_MT.config'
includeConfig 'conf/modules/call_snv_deepvariant.config'
includeConfig 'conf/modules/call_snv_sentieon.config'
includeConfig 'conf/modules/call_sv_MT.config'
includeConfig 'conf/modules/call_sv_cnvnator.config'
includeConfig 'conf/modules/call_sv_germlinecnvcaller.config'
includeConfig 'conf/modules/call_sv_manta.config'
includeConfig 'conf/modules/call_sv_tiddit.config'
includeConfig 'conf/modules/postprocess_MT_calls.config'
includeConfig 'conf/modules/call_mobile_elements.config'
includeConfig 'conf/modules/annotate_mobile_elements.config'
includeConfig 'conf/modules/generate_clinical_set.config'
includeConfig 'conf/modules/variant_evaluation.config'
includeConfig 'conf/modules/subsample_mt.config'
includeConfig 'conf/modules/annotate_rhocallviz.config'
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
defaultIgnoreParams = ["genomes"]
monochromeLogs = params.monochrome_logs
help {
enabled = true
command = "nextflow run nf-core/raredisease -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
beforeText = """
-\033[2m----------------------------------------------------\033[0m-
\033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m
\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m
\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m
\033[0;32m`._,._,\'\033[0m
\033[0;35m nf-core/raredisease ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/raredisease/blob/master/CITATIONS.md
"""
}
summary {
beforeText = validation.help.beforeText
afterText = validation.help.afterText
}
}