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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/cutandrun Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
/*
*** Flow switching and result output ***
There are three keywords for controling program flow and results output:
- save_* - Specifies whether to save information to output
- skip_* - Specifies whether to skip a process of group of processes
- only_* - Only run the pipeline up to this point
*/
// Global default params, used in configs
params {
// References
genome = null
spikein_genome = "K12-MG1655" // a common E. coli strain, use "R64-1-1" for yeast (S. cerevisiae) spike-in, BDGP6 for the fruit fly (D. melanogaster)
gene_bed = null
blacklist = null
save_reference = false
only_genome = false
// Input and merging
input = null
save_merged_fastq = false
only_input = false
// Pre-align QC
skip_fastqc = false
only_preqc = false
// Trimming
clip_r1 = 0
clip_r2 = 0
three_prime_clip_r1 = 0
three_prime_clip_r2 = 0
trim_nextseq = 0
save_trimmed = false
skip_trimming = false
// Alignment
aligner = "bowtie2"
save_spikein_aligned = false
save_unaligned = false
only_alignment = false
save_align_intermed = false
end_to_end = true
// Filtering
minimum_alignment_q_score = 20
remove_mitochondrial_reads = false
mito_name = null
// Deduplication
skip_removeduplicates = false
dedup_target_reads = false
only_filtering = false
remove_linear_duplicates = false
// Read Normalisation
normalisation_mode = "Spikein"
normalisation_binsize = 50
normalisation_c = 10000
igg_scale_factor = 0.5
// Peak Caller default param
peakcaller = 'seacr'
// Peak Calling
use_control = true
only_peak_calling = false
extend_fragments = true
seacr_norm = 'non'
seacr_stringent = 'stringent'
seacr_peak_threshold = 0.05
macs2_pvalue = null
macs2_qvalue = 0.01
macs_gsize = 2700000000.0
macs2_narrow_peak = true
macs2_broad_cutoff = 0.1
// Consensus Peaks
consensus_peak_mode = 'group'
replicate_threshold = 1.0
// Reporting and Visualisation
skip_reporting = false
skip_igv = false
skip_heatmaps = false
skip_dt_qc = false
skip_peak_qc = false
skip_preseq = false
skip_multiqc = false
dump_scale_factors = false
igv_show_gene_names = true
igv_sort_by_groups = true
min_frip_overlap = 0.2
min_peak_overlap = 0.2
// Deeptools options
dt_heatmap_gene_bodylen = 5000
dt_heatmap_gene_beforelen = 3000
dt_heatmap_gene_afterlen = 3000
dt_heatmap_peak_beforelen = 3000
dt_heatmap_peak_afterlen = 3000
dt_qc_bam_binsize = 500
dt_qc_corr_method = "pearson"
fragment_size = 100 // PARAM NOT USED
dt_calc_all_matrix = true
// Boilerplate options
outdir = "./results"
publish_dir_mode = "copy"
multiqc_config = null
multiqc_title = null
multiqc_logo = null
multiqc_methods_description = null
email = null
email_on_fail = null
max_multiqc_email_size = "25.MB"
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
igenomes_base = "s3://ngi-igenomes/igenomes/"
igenomes_ignore = false
singularity_pull_docker_container = false
// Config options
custom_config_version = "master"
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_name = null
config_profile_description = null
config_profile_contact = null
config_profile_url = null
// Max resource options
max_memory = "128.GB"
max_cpus = 16
max_time = "240.h"
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'igenomes_base,genomes,callers,dedup_control_only,fragment_size,run_igv,run_multiqc,run_reporting,run_consensus_all,run_peak_calling,run_remove_dups,run_remove_linear_dups,run_mark_dups,run_read_filter,run_alignment,run_trim_galore_fastqc,run_cat_fastq,run_input_check,run_genome_prep,run_peak_qc,run_deeptools_qc,run_deeptools_heatmaps,run_preseq'
validationShowHiddenParams = false
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig "conf/base.config"
// Load resources.config by default for all pipelines
includeConfig "conf/resources.config"
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// // Load nf-core/cutandrun custom config
// try {
// includeConfig "${params.custom_config_base}/pipeline/cutandrun.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/cutandrun profiles: ${params.custom_config_base}/pipeline/cutandrun.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
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)'
}
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
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
laptop { includeConfig "conf/laptop.config" } // Sets up compute resources for local computing run
test { includeConfig "conf/test.config" } // Runs a single sample with an IgG control
test_fasta_only { includeConfig "conf/test_fasta_only.config" } // Runs a single sample with an IgG control but with no extra genome files just as bed files and black lists
test_no_genome { includeConfig "conf/test_no_genome.config" } // Runs the same as basic test but with no preset genome files, just the genome id
test_tech_reps { includeConfig "conf/test_tech_reps.config" } // Runs a single sample with two technical replicates and an IgG control
test_full_small { includeConfig "conf/test_full_small.config" } // Runs a full experimental configuration but with a small dataset
test_no_control { includeConfig "conf/test_no_control.config" } // Runs a single sample with NO IgG control
test_full { includeConfig "conf/test_full.config" } // Runs a full experimental dataset
test_full_multi { includeConfig "conf/test_full_multi.config" } // Runs a full experimental dataset with extra fake replicates to enable full reporting functionality
test_local_zip { includeConfig "conf/test_local_zip.config" } // Runs a single sample with an IgG control but that targets local, already downloaded compressed input files
test_full_small_local_zip { includeConfig "conf/test_full_small_local_zip.config" } // Runs a full experimental configuration but with a small dataset but that targets local, already downloaded compressed input files
test_linear_dedup { includeConfig "conf/test_linear_dedup.config" } // Runs a full experimental configuration including the removal of linear amplification duplicates
}
// 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 '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
// 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"]
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/cutandrun'
author = """Chris Cheshire, Charlotte West and Tamara Hodgetts"""
homePage = 'https://github.com/nf-core/cutandrun'
description = """Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis."""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '3.2.2'
doi = 'https://doi.org/10.5281/zenodo.5653535'
}
// Load flowswitch.config
includeConfig 'conf/flowswitch.config'
// 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
}
}
}