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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/airrflow Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input parameters
input = null
mode = "fastq"
miairr="$projectDir/assets/reveal/mapping_MiAIRR_BioSample_v1.3.1.tsv"
index_file = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/'
// ----------------------------
// sequencing protocol options
// ----------------------------
library_generation_method = null
race_linker = null
// Primer and UMI inputs
cprimers = null
vprimers = null
vprimer_start = 0
cprimer_start = 0
cprimer_position = 'R1'
primer_revpr = false
// UMI and primer handling
umi_position = 'R1'
umi_length = -1
umi_start = 0
// trimming options
trim_fastq = true
adapter_fasta = null
clip_r1 = 0
clip_r2 = 0
three_prime_clip_r1 = 0
three_prime_clip_r2 = 0
trim_nextseq = false
save_trimmed = false
// --------------------------
// sequence assembly options
// --------------------------
// Filter sequences
filterseq_q = 20
// Mask primers
primer_r1_maxerror = 0.2
primer_r2_maxerror = 0.2
primer_r1_mask_mode = 'cut'
primer_r2_mask_mode = 'cut'
maskprimers_align_race = false
maskprimers_align = false
maskprimers_extract = false
primer_r1_extract_len = 0
primer_r2_extract_len = 0
primer_maxlen = 50
// Build consensus
primer_consensus = 0.6
buildconsensus_maxerror = 0.1
buildconsensus_maxgap = 0.5
cluster_sets = true
// Assemble pairs
assemblepairs_sequential = false
// internal cregion
align_cregion = false
internal_cregion_sequences = null
cregion_maxlen = 100
cregion_maxerror = 0.3
cregion_mask_mode = 'tag'
// -----------------------
// vdj annotation options
// -----------------------
productive_only = true
reassign = true
reference_igblast = "${params.pipelines_testdata_base_path}database-cache/igblast_base.zip"
reference_fasta = "${params.pipelines_testdata_base_path}database-cache/imgtdb_base.zip"
fetch_imgt = false
save_databases = true
skip_alignment_filter = false
// -----------------------
// bulk filtering options
// -----------------------
remove_chimeric = false
detect_contamination = false
collapseby = 'sample_id'
// -----------------------
// clonal analysis options
// -----------------------
cloneby = 'subject_id'
crossby = 'subject_id'
singlecell = 'single_cell'
clonal_threshold = 'auto'
skip_all_clones_report = false
skip_report_threshold = false
// tree lineage options
lineage_tree_builder = 'raxml'
lineage_tree_exec = '/usr/local/bin/raxml-ng'
lineage_trees = false
// -----------------------
// reporting options
// -----------------------
skip_report = false
report_rmd = "$projectDir/assets/repertoire_comparison.Rmd"
report_css = "$projectDir/assets/nf-core_style.css"
report_logo = "$projectDir/assets/nf-core-airrflow_logo_light.png"
report_logo_img = "$projectDir/assets/nf-core-airrflow_logo_reports.png"
// -----------------------
// Single cell raw input options
// -----------------------
reference_10x = null
// -----------------------
// raw RNA seq input options
// -----------------------
cell_barcode_read = null
read_format = null
umi_read = null
// -----------------------
// generic nf-core options
// -----------------------
// References
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = true
// MultiQC options
skip_multiqc = false
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
help_full = false
show_hidden = false
version = false
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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'
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 {
conda.enabled = false
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 {
conda.enabled = false
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
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_tcr { includeConfig 'conf/test_tcr.config' }
test_no_umi { includeConfig 'conf/test_no_umi.config' }
test_assembled_hs { includeConfig 'conf/test_assembled_hs.config' }
test_assembled_mm { includeConfig 'conf/test_assembled_mm.config' }
test_raw_immcantation_devel { includeConfig 'conf/test_raw_immcantation_devel.config' }
test_assembled_immcantation_devel_hs { includeConfig 'conf/test_assembled_immcantation_devel_hs.config' }
test_assembled_immcantation_devel_mm { includeConfig 'conf/test_assembled_immcantation_devel_mm.config' }
test_nocluster { includeConfig 'conf/test_nocluster.config' }
test_fetchimgt { includeConfig 'conf/test_fetchimgt.config' }
test_10x_sc { includeConfig 'conf/test_10x_sc.config' }
test_clontech_umi { includeConfig 'conf/test_clontech_umi.config' }
test_maskprimers_extract { includeConfig 'conf/test_maskprimers_extract.config' }
test_maskprimers_align {includeConfig 'conf/test_maskprimers_align.config' }
test_nebnext_umi { includeConfig 'conf/test_nebnext_umi.config' }
test_rnaseq_bulk { includeConfig 'conf/test_rnaseq_bulk.config' }
test_rnaseq_sc { includeConfig 'conf/test_rnaseq_sc.config' }
nebnext_umi_tcr { includeConfig 'conf/nebnext_umi_tcr.config' }
nebnext_umi_bcr { includeConfig 'conf/nebnext_umi_bcr.config' }
clontech_umi_bcr { includeConfig 'conf/clontech_umi_bcr.config' }
clontech_umi_tcr { includeConfig 'conf/clontech_umi_tcr.config' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf-core/airrflow custom profiles from different institutions.
// Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/airrflow.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"
R_LIBS_SITE = "NULL"
R_LIBS_USER = "NULL"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Set bash options
process.shell = """\
bash
set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
"""
// 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/airrflow'
author = """Gisela Gabernet, Susanna Marquez, Alexander Peltzer"""
homePage = 'https://github.com/nf-core/airrflow'
description = """B and T cell repertoire analysis pipeline with the Immcantation framework."""
mainScript = 'main.nf'
nextflowVersion = '!>=24.04.2'
version = '4.2.0'
doi = 'https://doi.org/10.1371/journal.pcbi.1012265'
}
// 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"]
help {
enabled = true
command = "nextflow run $manifest.name -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 ${manifest.name} ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/${manifest.name}/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'