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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sanger-tol/metagenomeassembly Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
// Assembly options
enable_assembly = true
enable_metamdbg = true
// Assembly QC options
enable_rrna_prediction = true
rfam_rrna_cm = "${baseDir}/assets/rRNA.cm"
// Read mapping options
hic_mapping_cram_bin_size = 10000
hic_mapping_minq = 60
hic_mapping_merge_mode = "merge"
// Binning options
enable_binning = true
enable_metabat2 = true
enable_maxbin2 = true
enable_bin3c = true
enable_metator = true
minimum_contig_size = 3000
minimum_bin_size = 150000
minimum_hifi_perc_identity = 97
// Bin refinement options
enable_bin_refinement = true
enable_dastool = true
enable_magscot = true
hmm_gtdb_pfam = "${baseDir}/assets/gtdbtk_rel207_Pfam-A.hmm"
hmm_gtdb_tigrfam = "${baseDir}/assets/gtdbtk_rel207_tigrfam.hmm"
// BinQC options
enable_binqc = true
enable_checkm2 = true
checkm2_db = null
enable_trnascan_se = true
// Taxonomy options
enable_taxonomy = true
enable_gtdbtk = true
gtdbtk_db = null
gtdbtk_mash_db = null
gtdb_ar53_metadata = "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/ar53_metadata_r220.tsv.gz"
gtdb_bac120_metadata = "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/bac120_metadata_r220.tsv.gz"
gtdbtk_min_completeness = 50
gtdbtk_max_contamination = 10
ncbi_taxonomy_dir = null
// Summary options
enable_summary = true
completeness_score = 1
contamination_score = 0.5
// Config options
config_profile_name = null
config_profile_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
monochrome_logs = false
help = false
help_full = false
show_hidden = false
version = false
// Metagenomeassembly config options
mgasm_pipelines_testdata_base_path = 'https://tolit.cog.sanger.ac.uk/test-data/'
// Config options
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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
process {
resourceLimits = [
memory: 8.GB,
cpus : 4,
time : 1.h
]
}
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_withassembly { includeConfig 'conf/test_withassembly.config' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load sanger-tol/metagenomeassembly custom profiles from different institutions.
// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/metagenomeassembly.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"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}
manifest {
name = 'sanger-tol/metagenomeassembly'
contributors = [
[
name: 'Jim Downie',
affiliation: 'Wellcome Sanger Institute',
email: '[email protected]',
github: '@prototaxites',
contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: '0000-0002-7175-0533'
],
[
name: ' Will Eagles',
affiliation: 'Wellcome Sanger Institute',
email: '',
github: '@weaglesBio',
contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: ''
],
[
name: ' Noah Gettle',
affiliation: 'Wellcome Sanger Institute',
email: '',
github: '@gettl008',
contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: ''
],
]
homePage = 'https://github.com/sanger-tol/metagenomeassembly'
description = """Construct MAGs from long reads."""
mainScript = 'main.nf'
defaultBranch = 'main'
nextflowVersion = '!>=24.04.2'
version = '1.0.0dev'
doi = ''
}
// 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 sanger-tol/metagenomeassembly -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// includeConfig 'conf/co2footprint.config'