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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/rnavar Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Pipeline options
// Mandatory option
input = null // sample sheet
// Genome and reference options
genome = 'GRCh38'
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
save_reference = false
save_merged_fastq = false
// Sequence read information
read_length = 150 // Required for STAR to build index and align reads
// Alignment
aligner = 'star' // Only STAR is currently supported.
star_twopass = true
star_ignore_sjdbgtf = false // Ignore GTF file while creating index or alignment by STAR
star_max_memory_bamsort = 0 // STAR parameter limitBAMsortRAM to specify maximum RAM for sorting BAM
star_bins_bamsort = 50 // STAR parameter outBAMsortingBinsN to specify number of bins for sorting BAM
star_max_collapsed_junc = 1000000 // STAR parameter limitOutSJcollapsed to specify max number of collapsed junctions
seq_center = null
seq_platform = 'illumina' // Required for preparing for BAM headers for GATK to work
bam_csi_index = false
save_unaligned = false
save_align_intermeds = false
// Preprocessing of alignment
remove_duplicates = false
// Variant calling
no_intervals = false
// Variant annotation
annotate_tools = null // List of annotation tools to run - snpeff or vep or merge
annotation_cache = false // Annotation cache disabled
cadd_cache = null // CADD cache disabled
cadd_indels = null // No CADD InDels file
cadd_indels_tbi = null // No CADD InDels index
cadd_wg_snvs = null // No CADD SNVs file
cadd_wg_snvs_tbi = null // No CADD SNVs index
genesplicer = null // genesplicer disabled within VEP
snpeff_cache = null // No directory for snpEff cache
snpeff_db = null // No default db for snpeff
vep_cache = null // No directory for VEP cache
vep_genome = null // No default genome for VEP
vep_cache_version = null // No default cache version for VEP
// Skip steps
skip_baserecalibration = false
skip_intervallisttools = false
skip_variantfiltration = false
skip_variantannotation = false
// GATK intervallist parameters
gatk_interval_scatter_count = 25
//GATK haplotypecaller parameters
gatk_hc_call_conf = 20
//GATK variant filter parameters
gatk_vf_window_size = 35
gatk_vf_cluster_size = 3
gatk_vf_fs_filter = 30.0
gatk_vf_qd_filter = 2.0
// QC
skip_multiqc = false
// MultiQC options
multiqc_config = null
multiqc_title = null
max_multiqc_email_size = '25.MB'
// Boilerplate options
outdir = 'results'
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes'
enable_conda = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// Max resource options
// 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 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: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/rnavar custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/pipeline/rnavar.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/rnavar profiles: ${params.custom_config_base}/pipeline/rnavar.config")
}
// Load nf-core/rnavar custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/rnavar.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/rnavar profiles: ${params.custom_config_base}/pipeline/rnavar.config")
// }
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.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_${trace_timestamp}.html"
}
manifest {
name = 'nf-core/rnavar'
author = '@praveenraj2018'
homePage = 'https://github.com/nf-core/rnavar'
description = 'GATK4 RNA variant calling pipeline'
mainScript = 'main.nf'
nextflowVersion = '>=21.10.3'
version = '1.0.0'
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}