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nextflow.config
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/*
========================================================================================
nf-core/rnaseq Nextflow config file
========================================================================================
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
public_data_ids = null
skip_sra_fastq_download = false
// References
genome = null
transcript_fasta = null
additional_fasta = null
splicesites = null
gtf_extra_attributes = 'gene_name'
gtf_group_features = 'gene_id'
featurecounts_feature_type = 'exon'
featurecounts_group_type = 'gene_biotype'
gencode = false
save_reference = false
// UMI handling
with_umi = false
umitools_extract_method = 'string'
umitools_bc_pattern = null
save_umi_intermeds = 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
// Ribosomal RNA removal
remove_ribo_rna = false
save_non_ribo_reads = false
ribo_database_manifest = "${projectDir}/assets/rrna-db-defaults.txt"
// Alignment
aligner = 'star_salmon'
pseudo_aligner = null
seq_center = null
bam_csi_index = false
star_ignore_sjdbgtf = false
hisat2_build_memory = '200.GB' // Amount of memory required to build HISAT2 index with splice sites
stringtie_ignore_gtf = false
min_mapped_reads = 5
save_merged_fastq = false
save_unaligned = false
save_align_intermeds = false
skip_markduplicates = false
skip_alignment = false
// QC
skip_qc = false
skip_bigwig = false
skip_stringtie = false
skip_fastqc = false
skip_preseq = false
skip_dupradar = false
skip_qualimap = false
skip_rseqc = false
skip_biotype_qc = false
skip_deseq2_qc = false
skip_multiqc = false
deseq2_vst = false
rseqc_modules = 'bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication'
// Boilerplate options
outdir = './results'
publish_dir_mode = 'copy'
multiqc_config = null
multiqc_title = null
email = null
email_on_fail = null
max_multiqc_email_size = '25.MB'
plaintext_email = false
monochrome_logs = false
help = false
igenomes_base = 's3://ngi-igenomes/igenomes/'
tracedir = "${params.outdir}/pipeline_info"
igenomes_ignore = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,modules'
enable_conda = false
singularity_pull_docker_container = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = [:]
config_profile_name = null
config_profile_description = null
config_profile_contact = null
config_profile_url = null
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/rnaseq custom config
try {
includeConfig "${params.custom_config_base}/pipeline/rnaseq.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/rnaseq profiles: ${params.custom_config_base}/pipeline/rnaseq.config")
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
// Avoid this error:
// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
// Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
// once this is established and works well, nextflow might implement this behavior as new default.
docker.runOptions = '-u \$(id -u):\$(id -g)'
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_sra { includeConfig 'conf/test_sra.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${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_${trace_timestamp}.svg"
}
manifest {
name = 'nf-core/rnaseq'
author = 'Phil Ewels, Rickard Hammarén'
homePage = 'https://github.com/nf-core/rnaseq'
description = 'Nextflow RNA-Seq analysis pipeline, part of the nf-core community.'
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.0'
version = '3.1'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}