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nextflow.config
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nextflow.config
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params {
fq_map = "fastq_map.tsv"
parasite {
fasta = "$projectDir/ref/PlasmoDB-44_Pfalciparum3D7_Genome.fasta"
fasta_prefix = "$projectDir/ref/PlasmoDB-44_Pfalciparum3D7_Genome"
}
host{
fasta = ["$projectDir/ref/host/hg38.fasta"]
fasta_prefix = ["$projectDir/ref/host/hg38"]
}
// Original known_snps_unsorted.vcf has 944,270 SNPs (from previous lab members).
// The updated file is pf_crosses_v1/known_variants.vcf which has 66,121 variants (snp/indels)
// The later is generated following the MalariaGen Pf6 paper:
// MalariaGEN, et al. (2021). An open dataset of Plasmodium falciparum
// genome variation in 7,000 worldwide samples. Wellcome Open Res 6, 42.
// 10.12688/wellcomeopenres.16168.2.
known_sites = ["$projectDir/ref/pf_crosses_v1/known_variants.vcf"]
genome_intervals = [
"chromosomes": [ "Pf3D7_01_v3", "Pf3D7_02_v3", "Pf3D7_03_v3", "Pf3D7_04_v3", "Pf3D7_05_v3",
"Pf3D7_06_v3", "Pf3D7_07_v3", "Pf3D7_08_v3", "Pf3D7_09_v3", "Pf3D7_10_v3", "Pf3D7_11_v3",
"Pf3D7_12_v3", "Pf3D7_13_v3", "Pf3D7_14_v3", ],
"intervals": [
"Pf3D7_01_v3:1-459121", "Pf3D7_01_v3:459122-640851",
"Pf3D7_02_v3:1-448875", "Pf3D7_02_v3:448876-947102",
"Pf3D7_03_v3:1-599046", "Pf3D7_03_v3:599047-1067971",
"Pf3D7_04_v3:1-599045", "Pf3D7_04_v3:599046-1200490",
"Pf3D7_05_v3:1-456496", "Pf3D7_05_v3:456497-906340", "Pf3D7_05_v3:906341-1343557",
"Pf3D7_06_v3:1-479812", "Pf3D7_06_v3:479813-974069", "Pf3D7_06_v3:974070-1418242",
"Pf3D7_07_v3:1-317635", "Pf3D7_07_v3:317636-810481", "Pf3D7_07_v3:810482-1445207",
"Pf3D7_08_v3:1-300241", "Pf3D7_08_v3:300242-839582", "Pf3D7_08_v3:839583-1472805",
"Pf3D7_09_v3:1-606468", "Pf3D7_09_v3:606469-1243310", "Pf3D7_09_v3:1243311-1541735",
"Pf3D7_10_v3:1-592199", "Pf3D7_10_v3:592200-1120767", "Pf3D7_10_v3:1120768-1687656",
"Pf3D7_11_v3:1-457696", "Pf3D7_11_v3:457697-979940", "Pf3D7_11_v3:979941-1516077", "Pf3D7_11_v3:1516078-2038340",
"Pf3D7_12_v3:1-668701", "Pf3D7_12_v3:668702-1283920", "Pf3D7_12_v3:1283921-1769193", "Pf3D7_12_v3:1769194-2271494",
"Pf3D7_13_v3:1-546554", "Pf3D7_13_v3:546555-1169276", "Pf3D7_13_v3:1169277-1702600",
"Pf3D7_13_v3:1702601-2368558", "Pf3D7_13_v3:2368559-2925236",
"Pf3D7_14_v3:1-568024", "Pf3D7_14_v3:568025-1073306", "Pf3D7_14_v3:1073307-1605259",
"Pf3D7_14_v3:1605260-2121870", "Pf3D7_14_v3:2121871-2706733", "Pf3D7_14_v3:2706734-3291936",
]
]
// to allow specifying a key for the above map `genome_intervals`: "chromosomes" or "intervals"
split = "chromosomes"
// to allow the pipeline to stop before haplotypecaller process and just obtain bam coverage information
coverage_only = false
// to allow the pipeline to stop after haplotypecaller calls (without joint call)
gvcf_only = false
hard = true
hard_filters = [
[name: "QD.lt.2", filter: "QD<2.0"],
[name: "FS.gt.60", filter: "FS>60.0"],
[name: "MQ.lt.40", filter: "MQ<40.0"],
[name: "MQRankSum.lt.-12.5", filter: "MQRankSum<-12.5"],
[name: "ReadPosRankSum.lt.-8", filter: "ReadPosRankSum<-8.0"]
]
// vqsr is off by default, because the test data is too small and will cause error/crash
vqsr = false
vqsr_resources = [
[name: 'jacob2014_microarray_liftover', type: 'truth', prior: 15, vcf: "$projectDir/ref/jacob2014_chip_sites.vcf" ],
[name: 'Pfcross1_3d7_hb3_gatk_pass', type: 'training', prior: 12, vcf: "$projectDir/ref/pf_crosses_v1/pass_3d7_hb3.gatk.final.vcf.gz" ],
[name: 'Pfcross1_7g8_gb4_gatk_pass', type: 'training', prior: 12, vcf: "$projectDir/ref/pf_crosses_v1/pass_7g8_gb4.gatk.final.vcf.gz" ],
[name: 'Pfcross1_hb3_dd2_gatk_pass', type: 'training', prior: 12, vcf: "$projectDir/ref/pf_crosses_v1/pass_hb3_dd2.gatk.final.vcf.gz" ]
]
vqsr_opts = "-an QD -an FS -an SOR -an DP --max-gaussians 3 --mq-cap-for-logit-jitter-transform 70 "
vqsr_mode = "SNP"
// for coverage summary (here only consider autosomes)
genome_size_bp = 23292622
chrom_reg = "Pf3D7_[0-9]+_v3"
outdir = "result"
gatk_tmpdir = "${launchDir}/tmpdir"
}
env {
TMPDIR="${launchDir}/tmpdir"
}
profiles{
standard {
executor {
name = 'local'
queueSize = 10
pollInterval = '30 sec'
}
conda.enabled = true
process {
// For the simplicity of configuration, a yaml file is used. In this case,
// nextflow will install the snp_call_nf environment in a cache folder.
conda = "$projectDir/env/snp_call_nf.yaml"
// If the snp_call_fn environment is already installed,
// one can specify the full path to the existing environment folder.
// conda = "${CONDA_PREFIX_1}/envs/snp_call_nf"
cache = 'lenient'
errorStrategy = {task.attempt < 5 ? 'retry': 'ignore'}
maxRetries = 5
cpus = 1
memory = '5 GB'
withName: 'BOWTIE2.*' {
cpus = 3
}
withName: 'SAMTOOLS_FASTQ' {
cpus = 3
}
withName: 'GATK_GENOMICS_DB_IMPORT' {
cpus = 10
memory = '50 GB'
}
withName: 'GATK_GENOTYPE_GVCFS' {
cpus = 10
memory = '50 GB'
}
}
}
sge {
executor {
name = 'sge'
queueSize = 100
pollInterval = '30 sec'
}
conda.enabled = true
process {
// For the simplicity of configuration, a yaml file is used. In this case,
// nextflow will install the snp_call_nf environment in a cache folder.
conda = "$projectDir/env/snp_call_nf.yaml"
// If the snp_call_fn environment is already installed,
// one can specify the full path to the existing environment folder.
// conda = "${CONDA_PREFIX_1}/envs/snp_call_nf"
// Cache keys are created indexing input files path and size
// attributes (this policy provides a workaround for incorrect
// caching invalidation observed on shared file systems due to
// inconsistent files timestamps).
cache = 'lenient'
errorStrategy = {task.attempt < 5 ? 'retry': 'ignore'}
maxRetries = 5
cpus = 1
memory = '5 GB'
queue = "threaded.q"
penv = "thread"
clusterOptions = "-P toconnor-lab -cwd -V"
withName: "BOWTIE2.*" {
cpus = 3
}
withName: 'SAMTOOLS_FASTQ' {
cpus = 3
}
withName: 'GATK_GENOMICS_DB_IMPORT' {
cpus = 10
memory = '50 GB'
}
withName: 'GATK_GENOTYPE_GVCFS' {
cpus = 10
memory = '50 GB'
}
}
}
}
manifest {
name = 'snp_call_nf'
author = 'Bing Guo'
homePage = 'https://github.com/snp_call_nf'
description = 'Nextflow plasmodium SNP call pipeline'
mainScript = 'main.nf'
nextflowVersion = '>=21.04.0'
version = '0.1.1'
}
trace {
enabled = true
fields = 'task_id,hash,native_id,name,status,exit,realtime,%cpu,rss'
}