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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genomic-medicine-sweden/tomte Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
// References
genome = 'GRCh38'
gencode_annotation_version = 46
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = false
save_reference = true
fasta = null
fai = null
gtf = null
star_index = null
transcript_fasta = null
salmon_index = null
sequence_dict = null
skip_download_vep = true
skip_download_gnomad = true
vep_refs_download = null
// Main options
platform = 'illumina'
// Trimming
min_trimmed_length = 40
// Alignment
star_two_pass_mode = 'Basic'
skip_subsample_region = false
skip_downsample = false
num_reads = 120000000
seed_frac = 0.001
save_mapped_as_cram = true
// Variant calling
skip_variant_calling = false
variant_caller = 'bcftools'
bcftools_caller_mode = 'multiallelic'
skip_build_tracks = false
skip_stringtie = false
skip_drop_ae = false
skip_drop_as = false
skip_export_counts_drop = true
drop_group_samples_ae = 'outrider'
drop_group_samples_as = 'fraser'
drop_padjcutoff_ae = 0.05
drop_padjcutoff_as = 0.1
drop_zscorecutoff = 0
skip_vep = false
// Variant annotation
vep_cache_version = 112
vep_cache = null
vep_plugin_files = null
// QC options
skip_peddy = false
skip_calculate_hb_frac = false
hb_genes = null
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = "${projectDir}/assets/tomte_logo_light.png"
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = 'results'
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
help_full = false
show_hidden = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
charliecloud.registry = 'quay.io'
// Load igenomes.config if required
includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Set bash options
process.shell = """\
bash
set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
"""
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'genomic-medicine-sweden/tomte'
author = """Clinical Genomics Stockholm"""
homePage = 'https://github.com/genomic-medicine-sweden/tomte'
description = """Pipeline to analyse RNAseq from raredisease patients"""
mainScript = 'main.nf'
nextflowVersion = '!>=24.04.2'
version = '3.0.0'
doi = '10.5281/zenodo.10828946'
}
// Nextflow plugins
plugins {
id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
defaultIgnoreParams = ["genomes"]
help {
enabled = true
command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
beforeText = """
\033[0;34m
\033[0;34m----------------------------------------------------
\033[0;34m _____ __ __ _____ _ _
\033[0;34m / ____| \\/ |/ ____| | | | |
\033[0;34m | | __| \\ / | (___ ______ | |_ ___ _ __ ___ | |_ ___
\033[0;34m | | |_ | |\\/| |\\___ \\ |______| | __/ _ \\| '_ ` _ \\| __/ _ \
\033[0;34m | |__| | | | |____) | | || (_) | | | | | | || __/
\033[0;34m \\_____|_| |_|_____/ \\__\\___/|_| |_| |_|\\__\\___|
\033[0;34m----------------------------------------------------
\033[0;34m
"""
afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/${manifest.name}/blob/master/CITATIONS.md
"""
}
summary {
beforeText = validation.help.beforeText
afterText = validation.help.afterText
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules/alignment.config'
includeConfig 'conf/modules/allele_specific_calling.config'
includeConfig 'conf/modules/analyse_transcripts.config'
includeConfig 'conf/modules/annotate_snv.config'
includeConfig 'conf/modules/bam_qc.config'
includeConfig 'conf/modules/call_variants.config'
includeConfig 'conf/modules/download_references.config'
includeConfig 'conf/modules/igv_tracks.config'
includeConfig 'conf/modules/general_tomte.config'
includeConfig 'conf/modules/prepare_references.config'