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nextflow.config
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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
collapse_use_counts = false
// graph options
multiplet_recovery = true
leiden_iterations = 10
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_recovered_components = 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
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genomes,igenomes_base'
validationShowHiddenParams = false
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/pixelator custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/pixelator.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/pixelator profiles: ${params.custom_config_base}/pipeline/pixelator.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', 'defaults']
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
}
test { includeConfig 'conf/test.config' }
test_panel_v2 { includeConfig 'conf/test_panel_v2.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / 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'
// Nextflow plugins
plugins {
id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
// 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"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
// 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 = 'nf-core/pixelator'
author = """Pixelgen Technologies AB"""
homePage = 'https://github.com/nf-core/pixelator'
description = """Pipeline for analysis of Molecular Pixelation assays"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.3.1'
doi = '10.1101/2023.06.05.543770'
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}