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main.nf
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#! usr/bin/env nextflow
if( !nextflow.version.matches('>20.0') ) {
println "This workflow requires Nextflow version 20.0 or greater -- You are running version $nextflow.version"
println "On QUEST, you can use `module load python/anaconda3.6; source activate /projects/b1059/software/conda_envs/nf20_env`"
exit 1
}
nextflow.preview.dsl=2
// nextflow.enable.dsl=2
date = new Date().format( 'yyyyMMdd' )
/*
~ ~ ~ > * Parameters setup - GENERAL
*/
params.help = null
params.debug = null
download_vcf = null
params.finemap = true
params.species = "c_elegans"
params.bin_dir = "${workflow.projectDir}/bin" // this is different for gcp
params.data_dir = "${workflow.projectDir}/input_data" // this is different for gcp
params.out = "Analysis_Results-${date}"
params.fix = "fix"
// params.algorithm = 'inbred' //options: inbred, loco - now run both
// mediation only with c_elegans
if(params.species == "c_briggsae" || params.species == "c_tropicalis") {
med = false
} else {
med = params.mediation
}
/*
~ ~ ~ > * Parameters setup - MAPPING
*/
params.maf = 0.05
params.sparse_cut = 0.05
params.group_qtl = 1000
params.ci_size = 150
params.p3d = "TRUE"
params.genes = "${params.data_dir}/${params.species}/annotations/${params.species}.gff"
params.cores = 4
params.pca = true
// VCF parameters
if(params.debug) {
println """
*** Using debug mode ***
"""
// debug for now with small vcf
params.vcf = "${params.species}.test.vcf.gz"
params.traitfile = "${params.data_dir}/${params.species}/phenotypes/test_pheno.tsv"
vcf_file = Channel.fromPath("${params.data_dir}/${params.species}/genotypes/${params.vcf}")
vcf_index = Channel.fromPath("${params.data_dir}/${params.species}/genotypes/${params.vcf}.tbi")
// debug can use same vcf for impute and normal
impute_file = "${params.species}.test.vcf.gz" // just to print out for reference
impute_vcf = Channel.fromPath("${params.data_dir}/${params.species}/genotypes/${params.vcf}")
impute_vcf_index = Channel.fromPath("${params.data_dir}/${params.species}/genotypes/${params.vcf}.tbi")
ann_file = Channel.fromPath("${params.data_dir}/${params.species}/genotypes/WI.330_TEST.strain-annotation.tsv")
// for genomatrix profile
params.strains = "${params.data_dir}/${params.species}/phenotypes/strain_file.tsv"
} else if(params.gcp) {
// use the data directly from google on gcp - switch to elegansvariation.org for now?
// vcf_file = Channel.fromPath("gs://cendr-site-public-bucket/dataset_release/${params.species}/${params.vcf}/variation/WI.${params.vcf}.small.hard-filter.isotype.vcf.gz")
// vcf_index = Channel.fromPath("gs://cendr-site-public-bucket/dataset_release/${params.species}/${params.vcf}/variation/WI.${params.vcf}.small.hard-filter.isotype.vcf.gz.tbi")
vcf_file = Channel.fromPath("gs://elegansvariation.org/releases/${params.vcf}/variation/WI.${params.vcf}.small.hard-filter.isotype.vcf.gz")
vcf_index = Channel.fromPath("gs://elegansvariation.org/releases/${params.vcf}/variation/WI.${params.vcf}.small.hard-filter.isotype.vcf.gz.tbi")
impute_file = "WI.${params.vcf}.impute.isotype.vcf.gz" // just to print out for reference
// impute_vcf = Channel.fromPath("gs://cendr-site-public-bucket/dataset_release/${params.species}/${params.vcf}/variation/WI.${params.vcf}.impute.isotype.vcf.gz")
// impute_vcf_index = Channel.fromPath("gs://cendr-site-public-bucket/dataset_release/${params.species}/${params.vcf}/variation/WI.${params.vcf}.impute.isotype.vcf.gz.tbi")
impute_vcf = Channel.fromPath("gs://elegansvariation.org/releases/${params.vcf}/variation/WI.${params.vcf}.impute.isotype.vcf.gz")
impute_vcf_index = Channel.fromPath("gs://elegansvariation.org/releases/${params.vcf}/variation/WI.${params.vcf}.impute.isotype.vcf.gz.tbi")
// ann_file = Channel.fromPath("gs://cendr-site-public-bucket/dataset_release/${params.species}/${params.vcf}/variation/WI.${params.vcf}.strain-annotation.tsv")
ann_file = Channel.fromPath("gs://elegansvariation.org/releases/${params.vcf}/variation/WI.${params.vcf}.strain-annotation.tsv")
params.strains = "input_data/${params.species}/phenotypes/strain_file.tsv"
} else if(!params.vcf) {
// if there is no VCF date provided, pull the latest vcf from cendr.
params.vcf = "20220216"
vcf_file = "20220216 - CeNDR"
vcf_index = "20220216 - CeNDR"
impute_file = "20220216 - CeNDR"
download_vcf = true
} else {
// Check that params.vcf is valid
if("${params.vcf}" == "20220216" || "${params.vcf}" == "20210121" || "${params.vcf}" == "20200815" || "${params.vcf}" == "20180527" || "${params.vcf}" == "20170531" || "${params.vcf}" == "20210901" || "${params.vcf}" == "20210803") {
// if("${params.vcf}" in ["20210121", "20200815", "20180527", "20170531", "20210901"]) {
// check to make sure 20210901 is tropicalis
if("${params.vcf}" == "20210901") {
if("${params.species}" == "c_elegans" || "${params.species}" == "c_briggsae") {
println """
Error: VCF file (${params.vcf}) does not match species ${params.species} (should be c_tropicalis). Please enter a new vcf date or a new species to continue.
"""
System.exit(1)
}
}
// check to make sure vcf matches species for briggsae
if("${params.vcf}" == "20210803") {
if("${params.species}" == "c_elegans" || "${params.species}" == "c_tropicalis") {
println """
Error: VCF file (${params.vcf}) does not match species ${params.species} (should be c_briggsae). Please enter a new vcf date or a new species to continue.
"""
System.exit(1)
}
}
// check to make sure vcf matches species for elegans
if("${params.vcf}" == "20220216" || "${params.vcf}" == "20210121" || "${params.vcf}" == "20200815" || "${params.vcf}" == "20180527" || "${params.vcf}" == "20170531") {
if("${params.species}" == "c_briggsae" || "${params.species}" == "c_tropicalis") {
println """
Error: VCF file (${params.vcf}) does not match species ${params.species} (should be c_elegans). Please enter a new vcf date or a new species to continue.
"""
System.exit(1)
}
}
// use the vcf data from QUEST when a cendr date is provided
vcf_file = Channel.fromPath("/projects/b1059/data/${params.species}/WI/variation/${params.vcf}/vcf/WI.${params.vcf}.small.hard-filter.isotype.vcf.gz")
vcf_index = Channel.fromPath("/projects/b1059/data/${params.species}/WI/variation/${params.vcf}/vcf/WI.${params.vcf}.small.hard-filter.isotype.vcf.gz.tbi")
impute_file = "WI.${params.vcf}.impute.isotype.vcf.gz" // just to print out for reference
impute_vcf = Channel.fromPath("/projects/b1059/data/${params.species}/WI/variation/${params.vcf}/vcf/WI.${params.vcf}.impute.isotype.vcf.gz")
impute_vcf_index = Channel.fromPath("/projects/b1059/data/${params.species}/WI/variation/${params.vcf}/vcf/WI.${params.vcf}.impute.isotype.vcf.gz.tbi")
// check if cendr release date is before 20210121, use snpeff annotation
if("${params.vcf}" == "20200815" || "${params.vcf}" == "20180527" || "${params.vcf}" == "20170531") {
println "WARNING: Using snpeff annotation. To use BCSQ annotation, please use a newer vcf (2021 or later)"
ann_file = Channel.fromPath("/projects/b1059/data/${params.species}/WI/variation/${params.vcf}/vcf/WI.${params.vcf}.strain-annotation.snpeff.tsv")
} else {
ann_file = Channel.fromPath("/projects/b1059/data/${params.species}/WI/variation/${params.vcf}/vcf/WI.${params.vcf}.strain-annotation.tsv")
}
} else {
// check that vcf file exists, if it does, use it. If not, throw error
if (!file("${params.vcf}").exists()) {
println """
Error: VCF file (${params.vcf}) does not exist. Please provide a valid filepath or a valid CeNDR release date (i.e. 20210121)
"""
System.exit(1)
} else {
// if it DOES exist
println """
WARNING: Using a non-CeNDR VCF for analysis. Same VCF will be used for both GWA and fine mapping.
"""
vcf_file = Channel.fromPath("${params.vcf}")
vcf_index = Channel.fromPath("${params.vcf}.tbi")
impute_file = "${params.vcf}" // just to print out for reference
impute_vcf = Channel.fromPath("${params.vcf}")
impute_vcf_index = Channel.fromPath("${params.vcf}.tbi")
//choose default cendr date based on species for ann_file
if(params.species == "c_elegans") {
default_date = "20220216"
} else if(params.species == "c_briggsae") {
default_date = "20210803"
} else {
default_date = "20210901"
}
// this does not work for another species...
ann_file = Channel.fromPath("/projects/b1059/data/${params.species}/WI/variation/${default_date}/vcf/WI.${default_date}.strain-annotation.tsv")
}
}
}
if (params.help) {
log.info '''
O~~~ O~~ O~~ ~~
O~ O~~ O~~ O~~ O~~
O~~ O~~ O~~ O~~ O~~~ O~~ O~~ O~~ O~~ O~~~ O~~ O~~ O~~
O~~ O~~ O~~ O~ O~~ O~~ O~ O~~ O~~ O~~ O~~ O~~ O~~ O~~ O~~ O~~
O~~ O~ O~~O~~~~~ O~~ O~~ O~ O~~O~~ O~~ O~~ O~~ O~~ O~~ O~~ O~~
O~~ O~ ~~O~ O~~ O~ O~~O~~ O~~ O~~ O~~ O~~ O~~ O~~ O~~ O~~
O~~ O~~ O~~~~ O~~~ O~ O~~ O~~ O~~~ O~~ ~~ O~~~ O~~ O~~~O~~~ O~~
'''
log.info "----------------------------------------------------------------"
log.info " USAGE "
log.info "----------------------------------------------------------------"
log.info ""
log.info "nextflow main.nf --debug"
log.info "nextflow main.nf --traitfile input_data/${params.species}/phenotypes/PC1.tsv --vcf 20210121"
log.info ""
log.info "Profiles available:"
log.info "mappings Profile Perform GWA mappings with a provided trait file"
log.info "simulations Profile Perform phenotype simulations with GCTA"
log.info "gcp Profile Perform GWA mappings on GCP (used for cendr)"
log.info "genomatrix Profile Generate a genotype matrix given a set of strains"
log.info "mappings_docker Profile Perform GWA mappings using a docker container for reproducibility"
log.info "local Profile Perform GWA mappings using a docker container with low memory and cpu avail. (need --finemap false)"
log.info "----------------------------------------------------------------"
log.info " -profile mappings USAGE"
log.info "----------------------------------------------------------------"
log.info "----------------------------------------------------------------"
log.info "nextflow main.nf --vcf 20210121 --traitfile input_data/${params.species}/phenotypes/PC1.tsv -profile mappings"
log.info "----------------------------------------------------------------"
log.info "----------------------------------------------------------------"
log.info "Mandatory arguments:"
log.info "--traitfile String Name of file that contains phenotypes. File should be tab-delimited with the columns: strain trait1 trait2 ..."
log.info "--vcf String Generally a CeNDR release date (i.e. 20210121). Can also provide a user-specified VCF with index in same folder."
log.info "Optional arguments:"
log.info "--MAF, --maf String Minimum minor allele frequency to use for single-marker mapping (Default: 0.05)"
log.info "--lmm String Perform GCTA mapping with --fastGWA-lmm algorithm (Default: RUN, option to not run is null)"
log.info "--lmm-exact String Perform GCTA mapping with --fastGWA-lmm-exact algorithm (Default: RUN, option to not run is null)"
log.info "--sparse_cut String Any off-diagonal value in the genetic relatedness matrix greater than this is set to 0 (Default: 0.05)"
log.info "----------------------------------------------------------------"
log.info " -profile simulations USAGE"
log.info "----------------------------------------------------------------"
log.info "----------------------------------------------------------------"
log.info "nextflow main.nf --vcf 20210121 -profile simulations"
log.info "----------------------------------------------------------------"
log.info "----------------------------------------------------------------"
log.info "Mandatory arguments:"
log.info "--simulate_nqtl File. A CSV file with the number of QTL to simulate per phenotype, one value per line (Default is located: input_data/all_species/simulate_nqtl.csv)"
log.info "--simulate_h2 File A CSV file with phenotype heritability, one value per line (Default is located: input_data/all_species/simulate_h2.csv)"
log.info "Optional arguments:"
log.info "--simulate_reps String The number of replicates to simulate per number of QTL and heritability (Default: 2)"
log.info "--simulate_maf File A CSV file where each line is a minor allele frequency threshold to test for simulations (Default: input_data/all_species/simulate_maf.csv)"
log.info "--simulate_eff File A CSV file where each line is an effect size to test for simulations (Default: input_data/all_species/simulate_effect_sizes.csv)"
log.info "--simulate_strains File A TSV file with two columns: the first is a name for the strain set and the second is a comma-separated strain list without spaces (Default: input_data/all_species/simulate_strains.csv)"
log.info "--simulate_qtlloc File A BED file with three columns: chromosome name (numeric 1-6), start postion, end postion. The genomic range specified is where markers will be pulled from to simulate QTL (Default: null [which defaults to using the whole genome to randomly simulate a QTL])"
log.info "----------------------------------------------------------------"
log.info "----------------------------------------------------------------"
log.info "Optional arguments (General):"
log.info "--out String Name of folder that will contain the results"
log.info "--e_mem String Value that corresponds to the amount of memory to allocate for eigen decomposition of chromosomes (DEFAULT = 100)"
log.info "Optional arguments (Marker):"
log.info "--sthresh String Significance threshold for QTL - Options: BF - for bonferroni correction, EIGEN - for SNV eigen value correction, or another number e.g. 4"
log.info "--group_qtl Integer If two QTL are less than this distance from each other, combine the QTL into one, (DEFAULT = 1000)"
log.info "--ci_size Integer Number of SNVs to the left and right of the peak marker used to define the QTL confidence interval, (DEFAULT = 150)"
log.info ""
log.info "--------------------------------------------------------"
log.info "Information describing the stucture of the input files can be located in input_files/README.txt"
log.info ""
log.info ""
log.info "Flags:"
log.info "--help Display this message"
log.info ""
log.info "--------------------------------------------------------"
log.info ""
log.info " Required software packages to be in users path"
log.info "BCFtools v1.9"
log.info "plink v1.9"
log.info "R-cegwas2 Found on GitHub"
log.info "R-tidyverse v1.2.1"
log.info "R-correlateR Found on GitHub"
log.info "R-rrBLUP v4.6"
log.info "R-sommer v3.5"
log.info "R-RSpectra v0.13-1"
log.info "R-ggbeeswarm v0.6.0"
log.info "--------------------------------------------------------"
exit 1
} else {
log.info '''
O~~~ O~~ O~~ ~~
O~ O~~ O~~ O~~ O~~
O~~ O~~ O~~ O~~ O~~~ O~~ O~~ O~~ O~~ O~~~ O~~ O~~ O~~
O~~ O~~ O~~ O~ O~~ O~~ O~ O~~ O~~ O~~ O~~ O~~ O~~ O~~ O~~ O~~
O~~ O~ O~~O~~~~~ O~~ O~~ O~ O~~O~~ O~~ O~~ O~~ O~~ O~~ O~~ O~~
O~~ O~ ~~O~ O~~ O~ O~~O~~ O~~ O~~ O~~ O~~ O~~ O~~ O~~ O~~
O~~ O~~ O~~~~ O~~~ O~ O~~ O~~ O~~~ O~~ ~~ O~~~ O~~ O~~~O~~~ O~~
'''
log.info ""
log.info "Trait File = ${params.traitfile}"
log.info "Strain File = ${params.strains}"
log.info "Species = ${params.species}"
log.info ""
log.info "VCF = ${params.vcf}"
log.info "Impute VCF = ${impute_file}"
log.info ""
log.info "Significance Threshold = ${params.sthresh}"
log.info "Result Directory = ${params.out}"
log.info "Minor allele frequency = ${params.maf}"
log.info "Mediation run? = ${med}"
log.info ""
}
// Includes
include {pull_vcf; fix_strain_names_bulk; fix_strain_names_alt; vcf_to_geno_matrix; chrom_eigen_variants; collect_eigen_variants} from './modules/setup.nf'
include {prepare_gcta_files; gcta_grm; gcta_lmm_exact_mapping; gcta_intervals_maps; gcta_lmm_exact_mapping_nopca} from './modules/mapping.nf'
include {mediation_data; multi_mediation; simple_mediation; summary_mediation} from './modules/mediation.nf'
include {summarize_mapping; generate_plots; LD_between_regions; prep_ld_files; gcta_fine_maps; divergent_and_haplotype; html_report_main} from './modules/post-mapping.nf'
include {prepare_simulation_files; chrom_eigen_variants_sims; collect_eigen_variants_sims; simulate_effects_loc; simulate_effects_genome; simulate_map_phenotypes; get_gcta_intervals} from './modules/simulations.nf'
/*
~ ~ ~ > * WORKFLOW
*/
workflow {
// if no VCF is provided, download the latest version from CeNDR
if(download_vcf) {
pull_vcf()
vcf_file = pull_vcf.out.hard_vcf
vcf_index = pull_vcf.out.hard_vcf_index
impute_vcf = pull_vcf.out.impute_vcf
impute_vcf_index = pull_vcf.out.impute_vcf_index
ann_file = pull_vcf.out.ann_vcf
}
// for mapping
if(params.maps) {
// Fix strain names
Channel.fromPath("${params.traitfile}")
.combine(Channel.fromPath("${params.data_dir}/${params.species}/isotypes/strain_isotype_lookup.tsv"))
.combine(Channel.fromPath("${params.bin_dir}/Fix_Isotype_names_bulk.R"))
.combine(Channel.from("${params.fix}")) | fix_strain_names_bulk
traits_to_map = fix_strain_names_bulk.out.fixed_strain_phenotypes
.flatten()
.map { file -> tuple(file.baseName.replaceAll(/pr_/,""), file) }
// Genotype matrix
pheno_strains = fix_strain_names_bulk.out.phenotyped_strains_to_analyze
vcf_file.combine(vcf_index)
.combine(pheno_strains) | vcf_to_geno_matrix
// EIGEN
contigs = Channel.from(["I", "II", "III", "IV", "V", "X"])
contigs.combine(vcf_to_geno_matrix.out)
.combine(Channel.fromPath("${params.bin_dir}/Get_GenoMatrix_Eigen.R")) | chrom_eigen_variants
chrom_eigen_variants.out.collect() | collect_eigen_variants
// GWAS mapping
if(params.pca) {
mapping_output = pheno_strains
.combine(traits_to_map)
.combine(vcf_file.combine(vcf_index))
.combine(Channel.fromPath("${params.data_dir}/all_species/rename_chromosomes")) | prepare_gcta_files | gcta_grm | gcta_lmm_exact_mapping
} else {
mapping_output = pheno_strains
.combine(traits_to_map)
.combine(vcf_file.combine(vcf_index))
.combine(Channel.fromPath("${params.data_dir}/all_species/rename_chromosomes")) | prepare_gcta_files | gcta_grm | gcta_lmm_exact_mapping_nopca
}
// process GWAS mapping
traits_to_map
.combine(collect_eigen_variants.out)
.combine(vcf_to_geno_matrix.out)
.combine(Channel.from("${params.p3d}"))
.combine(Channel.from("${params.sthresh}"))
.combine(Channel.from("${params.group_qtl}"))
.combine(Channel.from("${params.ci_size}"))
.join(mapping_output)
.combine(Channel.fromPath("${params.bin_dir}/Find_Aggregate_Intervals_Maps.R")) | gcta_intervals_maps
// plot
gcta_intervals_maps.out.maps_to_plot
.combine(Channel.fromPath("${params.bin_dir}/pipeline.plotting.mod.R")) | generate_plots
// LD b/w regions
gcta_intervals_maps.out.maps_to_plot
.combine(Channel.fromPath("${params.bin_dir}/LD_between_regions.R")) | LD_between_regions
// summarize all peaks
peaks_inbred = gcta_intervals_maps.out.qtl_peaks_inbred
.collectFile(keepHeader: true, name: "QTL_peaks_inbred.tsv", storeDir: "${params.out}/INBRED/Mapping/Processed")
peaks_loco = gcta_intervals_maps.out.qtl_peaks_loco
.collectFile(keepHeader: true, name: "QTL_peaks_loco.tsv", storeDir: "${params.out}/LOCO/Mapping/Processed")
peaks_inbred
.combine(peaks_loco)
.combine(Channel.fromPath("${params.data_dir}/${params.species}/genotypes/${params.species}_chr_lengths.tsv"))
.combine(Channel.fromPath("${params.bin_dir}/summarize_mappings.R")) | summarize_mapping
// run mediation with gaotian's eqtl
if(med) {
File transcripteqtl_all = new File("${params.data_dir}/${params.species}/phenotypes/expression/eQTL6545forMed.tsv")
transcript_eqtl = transcripteqtl_all.getAbsolutePath()
traits_to_mediate = fix_strain_names_bulk.out.fixed_strain_phenotypes
.flatten()
.map { file -> tuple(file.baseName.replaceAll(/pr_/,""), file) }
// combine inbred and loco qtl peaks for mediation
peaks_inbred
.splitCsv(sep: '\t', skip: 1)
.map { tch,marker,logPvalue,TRAIT,tstart,tpeak,tend,peak_id,h2 -> [TRAIT,tch,tstart,tpeak,tend,logPvalue,peak_id,h2,marker] }
.combine(Channel.from("inbred"))
.mix(peaks_loco
.splitCsv(sep: '\t', skip: 1)
.map { tch,marker,logPvalue,TRAIT,tstart,tpeak,tend,peak_id,h2 -> [TRAIT,tch,tstart,tpeak,tend,logPvalue,peak_id,h2,marker] }
.combine(Channel.from("loco")))
.combine(traits_to_mediate, by: 0)
.combine(Channel.from(transcript_eqtl))
.combine(Channel.fromPath("${params.bin_dir}/mediaton_input.R")) | mediation_data
mediation_data.out
.combine(vcf_to_geno_matrix.out)
.combine(Channel.fromPath("${params.data_dir}/${params.species}/phenotypes/expression/tx5291exp_st207.tsv"))
.combine(Channel.fromPath("${params.bin_dir}/multi_mediation.R")) | multi_mediation
multi_mediation.out.eQTL_gene
.splitCsv(sep: '\t')
.combine(mediation_data.out, by: [0,1,2,3])
.combine(vcf_to_geno_matrix.out)
.combine(Channel.fromPath("${params.data_dir}/${params.species}/phenotypes/expression/tx5291exp_st207.tsv"))
.combine(Channel.fromPath("${params.bin_dir}/simple_mediation.R")) | simple_mediation
// peaks_inbred
// .splitCsv(sep: '\t', skip: 1)
// .map { tch,marker,logPvalue,TRAIT,tstart,tpeak,tend,peak_id,h2 -> [TRAIT,tch,tstart,tpeak,tend,logPvalue,peak_id,h2,marker] }
// .combine(Channel.from("inbred"))
// .mix(peaks_loco
// .splitCsv(sep: '\t', skip: 1)
// .map { tch,marker,logPvalue,TRAIT,tstart,tpeak,tend,peak_id,h2 -> [TRAIT,tch,tstart,tpeak,tend,logPvalue,peak_id,h2,marker] }
// .combine(Channel.from("loco")))
multi_mediation.out.result_multi_mediate
.groupTuple(by: [0,1])
.join(simple_mediation.out.groupTuple(by: [0,1]), by: [0,1], remainder: true)
.combine(Channel.fromPath("${params.bin_dir}/summary_mediation.R")) | summary_mediation
// traits_to_mediate
// .combine(Channel.fromPath("${params.bin_dir}/summary_mediation.R"))
// .combine(simple_mediation.out.collect().toList())
// .combine(multi_mediation.out.result_multi_mediate.collect().toList()).view() | summary_mediation
}
// easiest case: don't run finemap, divergent, or html if params.finemap = false
if(params.finemap) {
// prep LD files
peaks_inbred
.splitCsv(sep: '\t', skip: 1)
.combine(Channel.from("inbred"))
.join(generate_plots.out.maps_from_plot_inbred, by: 3)
.mix(peaks_loco
.splitCsv(sep: '\t', skip: 1)
.combine(Channel.from("loco"))
.join(generate_plots.out.maps_from_plot_loco, by: 3))
.combine(impute_vcf.combine(impute_vcf_index))
.combine(pheno_strains)
.combine(Channel.fromPath("${params.data_dir}/all_species/rename_chromosomes")) | prep_ld_files
//fine mapping
prep_ld_files.out.finemap_preps
.combine(ann_file)
.combine(Channel.fromPath("${params.genes}"))
.combine(Channel.fromPath("${params.bin_dir}/Finemap_QTL_Intervals.R"))
.combine(Channel.fromPath("${params.bin_dir}/plot_genes.R"))
.combine(gcta_grm.out, by: 0) | gcta_fine_maps
// divergent regions and haplotypes
// only for elegans right now
if(params.species == "c_elegans") {
peaks_inbred
.combine(Channel.from("inbred"))
.mix(peaks_loco
.combine(Channel.from("loco")))
.combine(Channel.fromPath("${params.data_dir}/${params.species}/isotypes/divergent_bins.bed"))
.combine(Channel.fromPath("${params.data_dir}/${params.species}/isotypes/divergent_df_isotype.bed"))
.combine(Channel.fromPath("${params.data_dir}/${params.species}/isotypes/haplotype_df_isotype.bed"))
.combine(Channel.fromPath("${params.data_dir}/${params.species}/isotypes/div_isotype_list.txt")) | divergent_and_haplotype
if(med) {
// generate main html report
// Note: the order things get added matters, because if there is no QTL/fine mapping it will produce errors
peaks_inbred
.combine(peaks_loco)
.combine(traits_to_map) // trait names)
.combine(fix_strain_names_bulk.out.strain_issues) // strain issues file
.combine(collect_eigen_variants.out) // independent tests
.combine(vcf_to_geno_matrix.out) // genotype matrix
.combine(Channel.fromPath("${params.bin_dir}/NemaScan_Report_main.Rmd"))
.combine(Channel.fromPath("${params.bin_dir}/NemaScan_Report_region_template.Rmd"))
.combine(Channel.fromPath("${params.bin_dir}/render_markdown.R"))
.combine(Channel.fromPath("${params.bin_dir}/NemaScan_Report_algorithm_template.Rmd"))
.combine(Channel.from(med)) // true or false - plot mediaton?
.combine(Channel.from("${params.species}"))
.combine(divergent_and_haplotype.out.div_hap_table_inbred)
.combine(divergent_and_haplotype.out.div_hap_table_loco)
.join(gcta_intervals_maps.out.for_html, by: 2) // processed mapping data
.join(gcta_fine_maps.out.finemap_html_inbred, remainder: true) // fine mapping data
.join(gcta_fine_maps.out.finemap_html_loco, remainder: true)
.join(prep_ld_files.out.finemap_LD_inbred, remainder: true)
.join(prep_ld_files.out.finemap_LD_loco, remainder: true)
.join(summary_mediation.out.final_mediation_inbred, remainder: true)
.join(summary_mediation.out.final_mediation_loco, remainder: true) | html_report_main // more finemap data prep
} else {
// generate main html report
peaks_inbred
.combine(peaks_loco)
.combine(traits_to_map) // trait names)
.combine(fix_strain_names_bulk.out.strain_issues) // strain issues file
.combine(collect_eigen_variants.out) // independent tests
.combine(vcf_to_geno_matrix.out) // genotype matrix
.combine(Channel.fromPath("${params.bin_dir}/NemaScan_Report_main.Rmd"))
.combine(Channel.fromPath("${params.bin_dir}/NemaScan_Report_region_template.Rmd"))
.combine(Channel.fromPath("${params.bin_dir}/render_markdown.R"))
.combine(Channel.fromPath("${params.bin_dir}/NemaScan_Report_algorithm_template.Rmd"))
.combine(Channel.from(med)) // true or false - plot mediaton?
.combine(Channel.from("${params.species}"))
.combine(divergent_and_haplotype.out.div_hap_table_inbred)
.combine(divergent_and_haplotype.out.div_hap_table_loco)
.join(gcta_intervals_maps.out.for_html, by: 2) // processed mapping data
.join(gcta_fine_maps.out.finemap_html_inbred, remainder: true) // fine mapping data
.join(gcta_fine_maps.out.finemap_html_loco, remainder: true)
.join(prep_ld_files.out.finemap_LD_inbred, remainder: true)
.join(prep_ld_files.out.finemap_LD_loco, remainder: true) | html_report_main
}
} else {
// generate main html report
peaks_inbred
.combine(peaks_loco)
.combine(traits_to_map) // trait names)
.combine(fix_strain_names_bulk.out.strain_issues) // strain issues file
.combine(collect_eigen_variants.out) // independent tests
.combine(vcf_to_geno_matrix.out) // genotype matrix
.combine(Channel.fromPath("${params.bin_dir}/NemaScan_Report_main.Rmd"))
.combine(Channel.fromPath("${params.bin_dir}/NemaScan_Report_region_template.Rmd"))
.combine(Channel.fromPath("${params.bin_dir}/render_markdown.R"))
.combine(Channel.fromPath("${params.bin_dir}/NemaScan_Report_algorithm_template.Rmd"))
.combine(Channel.from(med)) // true or false - plot mediaton?
.combine(Channel.from("${params.species}"))
// don't have divergent files, so make them fake lol
.combine(Channel.from("${params.species}")).combine(Channel.from("${params.species}"))
.combine(Channel.from("${params.species}")).combine(Channel.from("${params.species}"))
.combine(Channel.from("${params.species}")).combine(Channel.from("${params.species}"))
.combine(Channel.from("${params.species}")).combine(Channel.from("${params.species}"))
.combine(Channel.from("${params.species}"))
.join(gcta_intervals_maps.out.for_html, by: 2) // processed mapping data
.join(gcta_fine_maps.out.finemap_html_inbred, remainder: true) // fine mapping data
.join(gcta_fine_maps.out.finemap_html_loco, remainder: true)
.join(prep_ld_files.out.finemap_LD_inbred, remainder: true)
.join(prep_ld_files.out.finemap_LD_loco, remainder: true) | html_report_main // more finemap data prep
}
}
} else if(params.matrix) {
// only run geno matrix step - and fix isotype names if needed
Channel.fromPath("${params.strains}")
.combine(Channel.fromPath("${params.data_dir}/${params.species}/isotypes/strain_isotype_lookup.tsv"))
.combine(Channel.fromPath("${params.bin_dir}/Fix_Isotype_names_alt.R"))
.combine(Channel.from("${params.fix}")) | fix_strain_names_alt
pheno_strains = fix_strain_names_alt.out.phenotyped_strains_to_analyze
vcf_file.combine(vcf_index)
.combine(pheno_strains) | vcf_to_geno_matrix
} else if(params.simulate) {
// for simulations
File pop_file = new File(params.simulate_strains);
Channel.from(pop_file.collect { it.tokenize( ' ' ) })
.map { SM, STRAINS -> [SM, STRAINS] }
.combine(vcf_file.combine(vcf_index))
.combine(Channel.fromPath("${params.data_dir}/all_species/rename_chromosomes"))
.combine(Channel.fromPath("${params.simulate_maf}").splitCsv()) | prepare_simulation_files
// eigen
contigs = Channel.from(["1", "2", "3", "4", "5", "6"])
contigs.combine(prepare_simulation_files.out.sim_geno)
.combine(Channel.fromPath("${params.bin_dir}/Get_GenoMatrix_Eigen.R")) | chrom_eigen_variants_sims
chrom_eigen_variants_sims.out.sim_geno_eigen_join
.groupTuple(by:[0,1,2]).
join(chrom_eigen_variants_sims.out.sim_geno_meta, by:[0,1,2]) | collect_eigen_variants_sims
// simulate qtl or genome
if(params.simulate_qtlloc){
collect_eigen_variants_sims.out
.combine(Channel.fromPath("${params.simulate_nqtl}").splitCsv())
.combine(Channel.fromPath("${params.simulate_qtlloc}"))
.combine(Channel.fromPath("${params.simulate_eff}").splitCsv())
.combine(Channel.from(1..params.simulate_reps))
.combine(Channel.fromPath("${params.bin_dir}/create_causal_QTLs.R")) | simulate_effects_loc
sim_phen_inputs = simulate_effects_loc.out
} else {
collect_eigen_variants_sims.out
.combine(Channel.fromPath("${params.simulate_nqtl}").splitCsv())
.combine(Channel.fromPath("${params.simulate_eff}").splitCsv())
.combine(Channel.from(1..params.simulate_reps))
.combine(Channel.fromPath("${params.bin_dir}/create_causal_QTLs.R")) | simulate_effects_genome
sim_phen_inputs = simulate_effects_genome.out
}
sim_phen_inputs
.combine(Channel.fromPath("${params.simulate_h2}").splitCsv()) | simulate_map_phenotypes
// simulation mappings
simulate_map_phenotypes.out.gcta_intervals
.combine(Channel.from("${params.sthresh}"))
.combine(Channel.from("${params.group_qtl}"))
.combine(Channel.from("${params.ci_size}"))
.combine(Channel.fromPath("${params.bin_dir}/Aggregate_Mappings.R"))
.combine(Channel.fromPath("${params.bin_dir}/Find_Aggregate_Intervals.R"))
.combine(Channel.fromPath("${params.bin_dir}/Find_GCTA_Intervals.R"))
.combine(Channel.fromPath("${params.bin_dir}/Find_GCTA_Intervals_LOCO.R")) | get_gcta_intervals
}
}
/*
=====================================
~ > * * < ~
~ ~ > * * < ~ ~
~ ~ ~ > * GENERATE REPORT * < ~ ~ ~
~ ~ > * * < ~ ~
~ > * * < ~
=====================================
*/
workflow.onComplete {
summary = """
Pipeline execution summary
---------------------------
Completed at: ${workflow.complete}
Duration : ${workflow.duration}
Success : ${workflow.success}
workDir : ${workflow.workDir}
exit status : ${workflow.exitStatus}
Error report: ${workflow.errorReport ?: '-'}
Git info: $workflow.repository - $workflow.revision [$workflow.commitId]
{ Parameters }
---------------------------
Phenotype File = ${params.traitfile}
VCF = ${params.vcf}
Significance Threshold = ${params.sthresh}
P3D = ${params.p3d}
Threshold for grouping QTL = ${params.group_qtl}
Number of SNVs to define CI = ${params.ci_size}
Mapping = ${params.maps}
Simulation = ${params.simulate}
Simulate QTL effects = ${params.simulate_qtlloc}
Annotation = ${params.annotate}
Result Directory = ${params.out}
"""
println summary
}