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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/rnavar Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null // sample sheet
// References
genome = 'GRCh38'
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = false
save_reference = false
save_merged_fastq = false
feature_type = 'exon'
// Sequence read information
read_length = 150 // Required for STAR to build index and align reads
// Alignment
aligner = 'star' // Only STAR is currently supported.
star_twopass = true
star_ignore_sjdbgtf = false // Ignore GTF file while creating index or alignment by STAR
star_max_memory_bamsort = 0 // STAR parameter limitBAMsortRAM to specify maximum RAM for sorting BAM
star_bins_bamsort = 50 // STAR parameter outBAMsortingBinsN to specify number of bins for sorting BAM
star_max_collapsed_junc = 1000000 // STAR parameter limitOutSJcollapsed to specify max number of collapsed junctions
star_max_intron_size = null // STAR parameter alignIntronMax to specify the max intron size
seq_center = null
seq_platform = 'illumina' // Required for preparing for BAM headers for GATK to work
bam_csi_index = false
save_unaligned = false
save_align_intermeds = false
// Preprocessing of alignment
remove_duplicates = false
extract_umi = false
umitools_extract_method = 'string'
umitools_bc_pattern = null
umitools_bc_pattern2 = null
umitools_umi_separator = null
// Variant calling
no_intervals = false
// Variant annotation
annotate_tools = null // List of annotation tools to run - snpeff or vep or merge
download_cache = false // Do not download annotation cache
dbnsfp = null // No dbnsfp processed file
dbnsfp_consequence = null // No default consequence for dbnsfp plugin
dbnsfp_fields = "rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF" // Default fields for dbnsfp plugin
dbnsfp_tbi = null // No dbnsfp processed file index
outdir_cache = null // No default outdir cache
snpeff_cache = 's3://annotation-cache/snpeff_cache/'
spliceai_indel = null // No spliceai_indel file
spliceai_indel_tbi = null // No spliceai_indel file index
spliceai_snv = null // No spliceai_snv file
spliceai_snv_tbi = null // No spliceai_snv file index
use_annotation_cache_keys = false
vep_cache = 's3://annotation-cache/vep_cache/'
vep_custom_args = "--everything --filter_common --per_gene --total_length --offline --format vcf" // Default arguments for VEP
vep_dbnsfp = null // dbnsfp plugin disabled within VEP
vep_include_fasta = false // Don't use fasta file for annotation with VEP
vep_loftee = null // loftee plugin disabled within VEP
vep_out_format = "vcf"
vep_spliceai = null // spliceai plugin disabled within VEP
vep_spliceregion = null // spliceregion plugin disabled within VEP
// Skip steps
skip_baserecalibration = false
skip_intervallisttools = false
skip_variantfiltration = false
skip_variantannotation = false
skip_exon_bed_check = false
// GATK intervallist parameters
gatk_interval_scatter_count = 25
// GATK haplotypecaller parameters
gatk_hc_call_conf = 20
generate_gvcf = false
//GATK variant filter parameters
gatk_vf_window_size = 35
gatk_vf_cluster_size = 3
gatk_vf_fs_filter = 30.0
gatk_vf_qd_filter = 2.0
// QC
skip_multiqc = false
// 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
modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data'
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data'
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
trace_report_suffix = "${new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')}"
// 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' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf-core/rnavar custom profiles from different institutions.
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/rnavar.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", // Returns the status of the last command to exit..
"pipefail" // ..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/rnavar'
author = """Praveen Raj, Maxime U Garcia""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
contributors = [
[
name: 'Praveen Raj',
affiliation: '',
email: '',
github: '',
contribution: [],
orcid: ''
],
[
name: 'Maxime U Garcia',
affiliation: 'Seqera',
email: '[email protected]',
github: '@maxulysse',
contribution: ['author'],
orcid: '0000-0003-2827-9261'
],
[
name: 'Nicolas Vannieuwkerke',
affiliation: 'CMGG',
email: '[email protected]',
github: '@nvnieuwk',
contribution: ['maintainer'],
orcid: '0009-0003-5619-1555'
]
]
homePage = 'https://github.com/nf-core/rnavar'
description = """GATK4 RNA variant calling pipeline"""
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=24.04.2'
version = '2.0.0dev'
doi = '10.5281/zenodo.6669636'
}
// 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/rnavar -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/rnavar ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${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/rnavar/blob/master/CITATIONS.md
"""
}
summary {
beforeText = validation.help.beforeText
afterText = validation.help.afterText
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
includeConfig 'conf/modules/annotate.config'
includeConfig 'conf/modules/prepare_cache.config'