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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/multiplesequencealign Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
seqs = null
tools = null
templates_suffix = ".pdb"
pdbs_dir = null
tree = null
args_tree = null
aligner = null
args_aligner = null
// Preprocessing and validation
skip_validation = false
skip_preprocessing = false
skip_pdbconversion = false
// Alignment
build_consensus = false
// Stats
skip_stats = false
calc_sim = false
calc_seq_stats = true
extract_plddt = false
// Evaluation
skip_eval = false
calc_sp = true
calc_tc = true
calc_irmsd = false
calc_gaps = true
calc_tcs = false
skip_compression = false
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
skip_multiqc = false
// 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
// Shiny options
shiny_app = "${projectDir}/bin/shiny_app"
skip_shiny = false
// Visualisation options
skip_visualisation = false
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Schema validation default options
validate_params = true
// Resource options
use_gpu = false
}
// 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
docker.runOptions = params.use_gpu ? '--gpus all' : '-u $(id -u):$(id -g)'
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
arm {
docker.runOptions = params.use_gpu ? '-u $(id -u):$(id -g) --platform=linux/amd64 --gpus all' : '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
singularity.runOptions = params.use_gpu ? '--nv' : ""
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
singularity.pullTimeout = '60m'
}
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
apptainer.runOptions = params.use_gpu ? '--nv' : ""
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_tiny { includeConfig 'conf/test_tiny.config' }
test_pdb { includeConfig 'conf/test_pdb.config' }
test_no_sheet { includeConfig 'conf/test_no_sheet.config' }
test_conda { includeConfig 'conf/test_conda.config' }
easy_deploy { includeConfig 'conf/easy_deploy.config' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
// Load nf-core/multiplesequencealign custom profiles from different institutions.
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/multiplesequencealign.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'
// 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"
fields = 'task_id, hash,native_id,name,status,exit,realtime,%cpu,rss,peak_rss,vmem,peak_vmem,rchar,wchar,cpus,start'
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}
manifest {
name = 'nf-core/multiplesequencealign'
contributors = [
[
name: 'Luisa Santus',
affiliation: 'Centre for Genomic Regulation (CRG)',
email: '[email protected]',
github: '@luisas',
contribution: ['author', 'maintainer', 'contributor'],
orcid: 'https://orcid.org/0000-0002-5992-0771'
],
[
name: ' Jose Espinosa Carrasco',
affiliation: 'Centre for Genomic Regulation (CRG)',
email: '[email protected]',
github: '@joseespinosa',
contribution: ['author', 'maintainer', 'contributor'],
orcid: 'https://orcid.org/0000-0002-1541-042X'
],
[
name: ' Leon Rauschning',
affiliation: 'Ludwig Maximilian Universitaet (LMU)',
email: '[email protected]',
github: '@lrauschning',
contribution: ['author', 'contributor'],
orcid: ''
],
[
name: ' Alessio Vignoli',
affiliation: 'Centre for Genomic Regulation (CRG)',
email: '[email protected]',
github: '@alessiovignoli',
contribution: ['author', 'contributor'],
orcid: 'https://orcid.org/0000-0001-7131-2915'
],
[
name: ' Igor Trujnara',
affiliation: 'Centre for Genomic Regulation (CRG)',
email: '[email protected]',
github: '@itrujnara',
contribution: ['author', 'contributor'],
orcid: ''
],
]
homePage = 'https://github.com/nf-core/multiplesequencealign'
description = """Pipeline to run and benchmark multiple sequence alignment tools."""
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=24.10.4'
version = '1.1.0'
doi = 'https://doi.org/10.5281/zenodo.13889386'
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
id '[email protected]'
}
def co2_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
co2footprint {
traceFile = "${params.outdir}/pipeline_info/co2footprint_trace_${co2_timestamp}.txt"
reportFile = "${params.outdir}/pipeline_info/co2footprint_report_${co2_timestamp}.html"
summaryFile = "${params.outdir}/pipeline_info/co2footprint_summary_${co2_timestamp}.txt"
}
validation {
monochromeLogs = params.monochrome_logs
defaultIgnoreParams = ["genomes", "fasta", "igenomes_base", "genome"]
help {
enabled = true
command = "nextflow run nf-core/multiplesequencealign -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/multiplesequencealign ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${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/multiplesequencealign/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'