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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
urlpipe Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
outdir = "./results"
input_nanopore_preprocess = null
// target reference (amplicon)
ref = "./assets/IlluminaHsQ50FibTrim_Ref.fa" // path to reference file
ref_repeat_start = 69 // 1-based repeat start coordinate on reference
ref_repeat_end = 218 // 1-based repeaet end coordinate on reference
ref_repeat_unit = "CAG" // repeat unit on reference
// how to determine the length of the CAG repeat:
length_mode = "distance_count" // choose from "reference_align", "distance_count"
// reference_align = "assets/IlluminaMmQ50Trim_Ref.fa" // legacy: put inside prep_ref config
// UMI cutoff parameters
umi_cutoffs = '1,3,5,7,10,30,100' // 0 (no correction) will be added by default
umi_correction_method = "least_distance" // choose from "least_distance", "mode", "mean", "least_squared_distance"
// repeat_bins: used for plotting purpose (GET_SUMMARY::GET_BIN_PLOT)
repeat_bins = "[(0,50), (51,60), (61,137), (138,154), (155,1000)]" // number and range of bins to plot, per-bp based number, not per-repeat-unit based number
// allele number: if 1, need to provide length_cutoff_1_x in the sample sheet; if 2, need to provide both length_cutoff_1_x and length_cutoff_2_x
allele_number = 1
// run pipeline with which mode: "default", "merge" ("merge" means that R1 and R2 will be merged first), "nanopore" (long reads), "nanopore_preprocess". If "nanopore_preprocess", will process a single nanopore fastq file: trimming, count bc occurrence, split into either direction, demultiplex
mode = "default"
// Nanopore mode specific arguments:
// which reads to keep: "forward_only", "reverse_only", "both_forward_reverse"
filter_reads = "both_forward_reverse"
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '32.GB'
max_cpus = 16
max_time = '240.h'
// MultiQC options: not implemented
multiqc_config = null
multiqc_title = null
max_multiqc_email_size = '25.MB'
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'symlink'
publish_dir_fastq = 'symlink'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes'
enable_conda = false
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
mamba {
params.enable_conda = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
docker.runOptions = '-u \$(id -u):\$(id -g) --rm -v /Users:/Users -v /tmp:/tmp --platform linux/amd64'
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
lsf {
process {
executor = 'lsf'
clusterOptions = ''
queue = 'short'
}
}
local {
executor {
queueSize = 3 // to avoid freezing local computer
}
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.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"
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.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'test/urlpipe'
author = 'Kai Hu'
homePage = 'https://github.com/test/urlpipe'
description = 'UMI-based Repeat Length analysis pipeline.'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.3'
version = '1.0dev'
}
// Load base.config for all pipelines
includeConfig 'conf/base.config'
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}