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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/rnasplice Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
contrasts = null
source = 'fastq'
// References
genome = null
transcript_fasta = null
gtf_extra_attributes = 'gene_name'
gtf_group_features = 'gene_id'
gencode = false
save_reference = false
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = false
// Trimming
clip_r1 = null
clip_r2 = null
three_prime_clip_r1 = null
three_prime_clip_r2 = null
trim_nextseq = null
save_trimmed = false
skip_trimming = false
skip_trimgalore_fastqc = false
min_trimmed_reads = 10000
// Alignment
aligner = 'star_salmon'
pseudo_aligner = 'salmon'
bam_csi_index = false
seq_center = null
salmon_quant_libtype = null
star_ignore_sjdbgtf = false
skip_alignment = false
save_unaligned = false
save_align_intermeds = false
save_merged_fastq = false
// QC
skip_bigwig = true
skip_fastqc = false
// rMATs
rmats = true
rmats_splice_diff_cutoff = 0.0001
rmats_paired_stats = true
rmats_read_len = 40
rmats_novel_splice_site = false
rmats_min_intron_len = 50
rmats_max_exon_len = 500
// DEXSeq DEU
dexseq_exon = true
save_dexseq_annotation = false
gff_dexseq = null
alignment_quality = 10
aggregation = true
save_dexseq_plot = true
n_dexseq_plot = 10
// edgeR DEU
edger_exon = true
save_edger_plot = true
n_edger_plot = 10
// DEXSeq DTU
dexseq_dtu = true
dtu_txi = 'dtuScaledTPM'
// Miso
sashimi_plot = true
miso_genes = 'ENSG00000004961, ENSG00000005302, ENSG00000147403'
miso_genes_file = null
miso_read_len = 75
fig_width = 7
fig_height = 7
// DRIMSeq Filtering
min_samps_feature_expr = 2
min_samps_feature_prop = 2
min_samps_gene_expr = 4
min_feature_expr = 10
min_feature_prop = 0.1
min_gene_expr = 10
// SUPPA options
suppa = true
suppa_per_local_event = true
suppa_per_isoform = true
suppa_tpm = null
// SUPPA Generate events options
generateevents_pool_genes = true
generateevents_event_type = 'SE SS MX RI FL'
generateevents_boundary = 'S'
generateevents_threshold = 10
generateevents_exon_length = 100
psiperevent_total_filter = 0
// SUPPA Diffsplice options
diffsplice_local_event = true
diffsplice_isoform = true
diffsplice_method = 'empirical'
diffsplice_area = 1000
diffsplice_lower_bound = 0
diffsplice_gene_correction = true
diffsplice_paired = true
diffsplice_alpha = 0.05
diffsplice_median = false
diffsplice_tpm_threshold = 0
diffsplice_nan_threshold = 0
// SUPPA Cluster options
clusterevents_local_event = true
clusterevents_isoform = true
clusterevents_sigthreshold = null
clusterevents_dpsithreshold= 0.05
clusterevents_eps = 0.05
clusterevents_metric = 'euclidean'
clusterevents_separation = null
clusterevents_min_pts = 20
clusterevents_method = 'DBSCAN'
// MultiQC options
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
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/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genomes,igenomes_base'
validationShowHiddenParams = false
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/rnasplice custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/rnasplice.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/rnasplice profiles: ${params.custom_config_base}/pipeline/rnasplice.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
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
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_edger { includeConfig 'conf/test_edger.config' }
test_rmats { includeConfig 'conf/test_rmats.config' }
test_dexseq { includeConfig 'conf/test_dexseq.config' }
test_suppa { includeConfig 'conf/test_suppa.config' }
test_fastq { includeConfig 'conf/test_fastq.config' }
test_genome_bam { includeConfig 'conf/test_genome_bam.config' }
test_transcriptome_bam { includeConfig 'conf/test_transcriptome_bam.config' }
test_salmon_results { includeConfig 'conf/test_salmon_results.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
}
// 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']
// 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/rnasplice'
author = """Ben Southgate, James Ashmore"""
homePage = 'https://github.com/nf-core/rnasplice'
description = """Alternative splicing analysis using RNA-seq."""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.0.4'
doi = '10.5281/zenodo.8424632'
}
// 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
}
}
}