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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/pixelator Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
input_basedir = null
// Preqc options
trim_front = 0
trim_tail = 0
max_length = null
min_length = null
max_n_bases = 0
avg_qual = 20
dedup = false
remove_polyg = false
// adapterqc options
adapterqc_mismatches = 0.1
// demux options
demux_mismatches = 0.1
demux_min_length = null
// collapse options
markers_ignore = null
algorithm = 'adjacency'
max_neighbours = 60
collapse_mismatches = 2
collapse_min_count = 2
// graph options
multiplet_recovery = true
graph_max_refinement_recursion_depth = 5
graph_max_edges_to_split = 5
graph_min_count = 2
// annotate options
min_size = null
max_size = null
dynamic_filter = 'min'
aggregate_calling = true
// analysis options
compute_polarization = true
compute_colocalization = true
use_full_bipartite = false
polarization_transformation = "log1p"
polarization_min_marker_count = 5
polarization_n_permutations = 50
colocalization_transformation = "rate-diff"
colocalization_neighbourhood_size = 1
colocalization_n_permutations = 50
colocalization_min_region_count = 5
colocalization_min_marker_count = 5
// Output options
save_amplicon_reads = false
save_qc_passed_reads = false
save_qc_failed_reads = false
save_demux_processed_reads = false
save_demux_failed_reads = false
save_collapsed_reads = false
save_edgelist = false
save_annotate_dataset = false
save_raw_component_metrics = false
save_analysis_dataset = false
save_all = false
// layout options
no_node_marker_counts = false
layout_algorithm = "wpmds_3d"
// skip options
skip_report = false
skip_analysis = false
skip_layout = false
// Main pixelator container override
pixelator_container = 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/pixelator/'
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'
def container_env_options = [
"MPLCONFIGDIR": '/tmp/.config/matplotlib',
"NUMBA_CACHE_DIR": "/tmp/.numba_cache",
]
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)'
env = container_env_options
}
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
env = container_env_options
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
podman.runOptions = '--userns=keep-id'
env = container_env_options
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
env = container_env_options
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
env = container_env_options
}
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
env = container_env_options
}
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_panel_v2 { includeConfig 'conf/test_panel_v2.config' }
test_scsp_v1_immunology_v1 { includeConfig 'conf/test_scsp_v1_immunology_v1.config' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf-core/pixelator custom profiles from different institutions.
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/pixelator.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 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/pixelator'
// Keep both author and contributors fields for compatibility with Nextflow versions < 24.10.0
author = """Pixelgen Technologies AB""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
contributors = [
[
name: 'Florian De Temmerman',
affiliation: 'Pixelgen Technologies AB',
email: 'florian.detemmerman@pixelgen.com',
github: '@fbdtemme',
contribution: ["author", "maintainer"], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: '0009-0006-0086-2470'
],
[
name: 'Johan Dahlberg',
affiliation: 'Pixelgen Technologies AB',
email: 'johan.dahlberg@pixelgen.com',
github: '@johandahlberg',
contribution: ["contributor"], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: '0000-0001-6962-1460'
],
[
name: 'Alvaro Martinez Barrio',
affiliation: 'Pixelgen Technologies AB',
email: 'alvaro.martinez.barrio@pixelgen.com',
github: '@ambarrio',
contribution: ["contributor"], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: '0000-0001-5064-2093'
],
]
homePage = '/~https://github.com/nf-core/pixelator'
description = """Pipeline for analysis of Molecular Pixelation assays"""
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=24.04.2'
version = '1.4.0'
doi = '10.1101/2023.06.05.543770'
}
// 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"]
monochromeLogs = params.monochrome_logs
help {
enabled = true
command = "nextflow run nf-core/pixelator -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/pixelator ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${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/pixelator/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'