/*

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

nf-core/sarek Nextflow config file

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Default config options for all compute environments

----------------------------------------------------------------------------------------

*/

params {

// Workflow flags:

// Mandatory arguments

input = null // No default input

step = 'mapping' // Starts with mapping

// References

genome = 'GATK.GRCh38'

igenomes_base = 's3://ngi-igenomes/igenomes'

igenomes_ignore = false

save_reference = false // Built references not saved

build_only_index = false // Only build the reference indexes

download_cache = false // Do not download annotation cache

// Main options

no_intervals = false // Intervals will be built from the fasta file

nucleotides_per_second = 200000 // Default interval size

tools = null // No default Variant_Calling or Annotation tools

skip_tools = null // All tools (markduplicates + baserecalibrator + QC) are used by default

split_fastq = 50000000 // FASTQ files will not be split by default by FASTP

// Modify fastqs (trim/split) with FASTP

trim_fastq = false // No trimming

clip_r1 = 0

clip_r2 = 0

three_prime_clip_r1 = 0

three_prime_clip_r2 = 0

trim_nextseq = 0

save_trimmed = false

save_split_fastqs = false

// UMI tagged reads

umi_read_structure = null // no UMI

group_by_umi_strategy = 'Adjacency' // default strategy when running with UMI for GROUPREADSBYUMI

// Preprocessing

aligner = 'bwa-mem' // Default is bwa-mem, bwa-mem2 and dragmap can be used too

use_gatk_spark = null // GATK Spark implementation of their tools in local mode not used by default

save_mapped = false // Mapped BAMs not saved

save_output_as_bam = false // Output files from preprocessing are saved as bam and not as cram files

seq_center = null // No sequencing center to be written in read group CN field by aligner

seq_platform = 'ILLUMINA' // Default platform written in read group PL field by aligner

// Variant Calling

only_paired_variant_calling = false // if true, skips germline variant calling for normal-paired samples

ascat_ploidy = null // default value for ASCAT

ascat_min_base_qual = 20 // default value for ASCAT

ascat_min_counts = 10 // default value for ASCAT

ascat_min_map_qual = 35 // default value for ASCAT

ascat_purity = null // default value for ASCAT

cf_ploidy = "2" // default value for Control-FREEC

cf_coeff = 0.05 // default value for Control-FREEC

cf_contamination = 0 // default value for Control-FREEC

cf_contamination_adjustment = false // by default we are not using this in Control-FREEC

cf_mincov = 0 // ControlFreec default values

cf_minqual = 0 // ControlFreec default values

cf_window = null // by default we are not using this in Control-FREEC

cnvkit_reference = null // by default the reference is build from the fasta file

concatenate_vcfs = false // by default we don't concatenate the germline-vcf-files

ignore_soft_clipped_bases = false // no --dont-use-soft-clipped-bases for GATK Mutect2

wes = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers

joint_germline = false // g.vcf & joint germline calling are not run by default if HaplotypeCaller is selected

joint_mutect2 = false // if true, enables patient-wise multi-sample somatic variant calling

sentieon_haplotyper_emit_mode = "variant" // default value for Sentieon haplotyper

// Annotation

dbnsfp = null // No dbnsfp processed file

dbnsfp_consequence = null // No default consequence for dbnsfp plugin

dbnsfp_fields = "rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF" // Default fields for dbnsfp plugin

dbnsfp_tbi = null // No dbnsfp processed file index

outdir_cache = null // No default outdir cache

snpeff_cache = 's3://annotation-cache/snpeff_cache/'

spliceai_indel = null // No spliceai_indel file

spliceai_indel_tbi = null // No spliceai_indel file index

spliceai_snv = null // No spliceai_snv file

spliceai_snv_tbi = null // No spliceai_snv file index

use_annotation_cache_keys = false

vep_cache = 's3://annotation-cache/vep_cache/'

vep_custom_args = "--everything --filter_common --per_gene --total_length --offline --format vcf" // Default arguments for VEP

vep_dbnsfp = null // dbnsfp plugin disabled within VEP

vep_include_fasta = false // Don't use fasta file for annotation with VEP

vep_loftee = null // loftee plugin disabled within VEP

vep_out_format = "vcf"

vep_spliceai = null // spliceai plugin disabled within VEP

vep_spliceregion = null // spliceregion plugin disabled within VEP

// 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

test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek3'

// 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 = true

validationSchemaIgnoreParams = 'cf_ploidy,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/sarek custom profiles from different institutions.

try {

includeConfig "${params.custom_config_base}/pipeline/sarek.config"

} catch (Exception e) {

System.err.println("WARNING: Could not load nf-core/config/sarek profiles: ${params.custom_config_base}/pipeline/sarek.config")

}

profiles {

debug {

cleanup = false

dumpHashes = true

process.beforeScript = 'echo $HOSTNAME'

}

conda {

apptainer.enabled = false

charliecloud.enabled = false

conda.enabled = true

docker.enabled = false

podman.enabled = false

shifter.enabled = false

singularity.enabled = false

}

mamba {

apptainer.enabled = false

charliecloud.enabled = false

conda.enabled = true

conda.useMamba = true

charliecloud.enabled = false

docker.enabled = false

podman.enabled = false

shifter.enabled = false

singularity.enabled = false

}

docker {

apptainer.enabled = false

charliecloud.enabled = false

conda.enabled = false

docker.enabled = true

docker.userEmulation = { params.use_gatk_spark ? false : true }.call()

podman.enabled = false

shifter.enabled = false

singularity.enabled = false

}

arm {

docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'

}

singularity {

apptainer.enabled = false

charliecloud.enabled = false

conda.enabled = false

docker.enabled = false

podman.enabled = false

shifter.enabled = false

singularity.autoMounts = true

singularity.enabled = true

}

podman {

apptainer.enabled = false

charliecloud.enabled = false

conda.enabled = false

docker.enabled = false

podman.enabled = true

shifter.enabled = false

singularity.enabled = false

}

shifter {

apptainer.enabled = false

charliecloud.enabled = false

conda.enabled = false

docker.enabled = false

podman.enabled = false

shifter.enabled = true

singularity.enabled = false

}

charliecloud {

apptainer.enabled = false

charliecloud.enabled = true

conda.enabled = false

docker.enabled = false

podman.enabled = false

shifter.enabled = false

singularity.enabled = false

}

apptainer {

apptainer.enabled = true

apptainer.autoMounts = true

charliecloud.enabled = false

conda.enabled = false

docker.enabled = false

podman.enabled = false

shifter.enabled = false

singularity.enabled = false

}

gitpod {

executor.cpus = 4

executor.memory = 8.GB

executor.name = 'local'

}

// Basic test profile for CI

test { includeConfig 'conf/test.config' }

test_cache { includeConfig 'conf/test/cache.config' }

// Extra test profiles for full tests on AWS

test_full { includeConfig 'conf/test_full.config' }

test_full_germline { includeConfig 'conf/test_full_germline.config' }

// Extra test profiles for more complete CI

alignment_to_fastq { includeConfig 'conf/test/alignment_to_fastq.config' }

annotation { includeConfig 'conf/test/annotation.config' }

markduplicates_bam { includeConfig 'conf/test/markduplicates_bam.config' }

markduplicates_cram { includeConfig 'conf/test/markduplicates_cram.config' }

no_intervals { includeConfig 'conf/test/no_intervals.config' }

pair { includeConfig 'conf/test/pair.config' }

prepare_recalibration_bam { includeConfig 'conf/test/prepare_recalibration_bam.config' }

prepare_recalibration_cram { includeConfig 'conf/test/prepare_recalibration_cram.config' }

recalibrate_bam { includeConfig 'conf/test/recalibrate_bam.config' }

recalibrate_cram { includeConfig 'conf/test/recalibrate_cram.config' }

save_bam_mapped { includeConfig 'conf/test/save_bam_mapped.config' }

sentieon_dedup_bam { includeConfig 'conf/test/sentieon_dedup_bam.config' }

sentieon_dedup_cram { includeConfig 'conf/test/sentieon_dedup_cram.config' }

skip_bqsr { includeConfig 'conf/test/skip_bqsr.config' }

skip_markduplicates { includeConfig 'conf/test/skip_markduplicates.config' }

split_fastq { includeConfig 'conf/test/split_fastq.config' }

targeted { includeConfig 'conf/test/targeted.config' }

tools { includeConfig 'conf/test/tools.config' }

tools_germline { includeConfig 'conf/test/tools_germline.config' }

tools_somatic { includeConfig 'conf/test/tools_somatic.config' }

tools_somatic_ascat { includeConfig 'conf/test/tools_somatic_ascat.config' }

tools_tumoronly { includeConfig 'conf/test/tools_tumoronly.config' }

trimming { includeConfig 'conf/test/trimming.config' }

umi { includeConfig 'conf/test/umi.config' }

use_gatk_spark { includeConfig 'conf/test/use_gatk_spark.config' }

variantcalling_channels { includeConfig 'conf/test/variantcalling_channels.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' // Validation of pipeline parameters and creation of an input channel from a sample sheet

id 'nf-prov' // Provenance reports for pipeline runs

}

// 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"

}

prov {

enabled = true

file = "${params.outdir}/pipeline_info/manifest_${trace_timestamp}.bco.json"

}

manifest {

name = 'nf-core/sarek'

author = """Maxime Garcia, Szilveszter Juhos, Friederike Hanssen"""

homePage = 'https://github.com/nf-core/sarek'

description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing"""

mainScript = 'main.nf'

nextflowVersion = '!>=23.04.0'

version = '3.3.2'

doi = '10.12688/f1000research.16665.2, 10.1101/2023.07.19.549462, 10.5281/zenodo.3476425'

}

// Load modules.config for DSL2 module specific options

includeConfig 'conf/modules/modules.config'

// Load more modules specific config for DSL2 module specific options

// prepare reference

includeConfig 'conf/modules/prepare_cache.config'

includeConfig 'conf/modules/prepare_genome.config'

includeConfig 'conf/modules/prepare_intervals.config'

// preprocessing

includeConfig 'conf/modules/aligner.config'

includeConfig 'conf/modules/alignment_to_fastq.config'

includeConfig 'conf/modules/markduplicates.config'

includeConfig 'conf/modules/sentieon_dedup.config'

includeConfig 'conf/modules/prepare_recalibration.config'

includeConfig 'conf/modules/recalibrate.config'

includeConfig 'conf/modules/trimming.config'

includeConfig 'conf/modules/umi.config'

// variant calling

includeConfig 'conf/modules/ascat.config'

includeConfig 'conf/modules/cnvkit.config'

includeConfig 'conf/modules/controlfreec.config'

includeConfig 'conf/modules/deepvariant.config'

includeConfig 'conf/modules/freebayes.config'

includeConfig 'conf/modules/haplotypecaller.config'

includeConfig 'conf/modules/joint_germline.config'

includeConfig 'conf/modules/manta.config'

includeConfig 'conf/modules/mpileup.config'

includeConfig 'conf/modules/msisensorpro.config'

includeConfig 'conf/modules/mutect2.config'

includeConfig 'conf/modules/sentieon_haplotyper.config'

includeConfig 'conf/modules/sentieon_joint_germline.config'

includeConfig 'conf/modules/strelka.config'

includeConfig 'conf/modules/tiddit.config'

includeConfig 'conf/modules/post_variant_calling.config'

//annotate

includeConfig 'conf/modules/annotate.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

}

}

}