/
20231205_process_sims_ce192.nf
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20231205_process_sims_ce192.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 $nextflow.version"
println "On QUEST, you can use `module load python/anaconda3.6; source activate /projects/b1059/software/conda_envs/nf20_env`"
exit 1
}
nextflow.preview.dsl=2
// nextflow.enable.dsl=2
date = new Date().format( 'yyyyMMdd_HHmmss' )
params.bin_dir = "${workflow.projectDir}/bin" // this is different for gcp
params.out = "test_Analysis_Results-${date}"
sim_dir = "/projects/b1059/projects/Ryan/Caenorhabditis_GWAS/best_panel_subsample/20231017_CE_96.192_Alloutlier/20231024_CE_96.192_Alloutlier"
params.group_qtl = 1000
params.sthresh = "BF"
params.ci_size = 150
include {get_gcta_intervals; assess_sims_INBRED; assess_sims_LOCO} from './modules/simulations.nf'
workflow{
//create a channel from the Simulations folder for CE - WILL ONLY WORK WITH ON NQTL PARAMETER SIMULATIONS
//print status messages to the console
//process.statusCommand = "echo 'Running...'"
//pull the phenotypes file
effects_ch = Channel.fromPath("${sim_dir}/Simulations/gamma/5/Phenotypes/*_*_*_*_*_ce.192*.phen")
// pull out the simulation ID from the file name
.map{ file ->
def parts = file.getBaseName().split('_')
return tuple(parts[0], parts[1], parts[2], parts[3], parts[4], parts[5], parts[6], file)
}
//effects_ch.view()
//causal variant input channel
cv_ch = Channel.fromPath(
"${sim_dir}/Simulations/gamma/5/Phenotypes/*_*_*_*_*_ce.192*.par"
)
.map{ file ->
def parts = file.getBaseName().split('_')
return tuple(parts[0], parts[1], parts[2], parts[3], parts[4], parts[5], parts[6], file)
}
//cv_ch.view()
//create a channel for the raw mapping files
raw_mappings_inbred = Channel.fromPath("${sim_dir}/Simulations/gamma/5/Mappings/*_*_*_*_*_ce.192*_lmm-exact_inbred_pca.fastGWA")
// pull out the simulation ID from the file name
.map{ file ->
def parts = file.getBaseName().split('_')
// 1 - NQTL, 2 - SIMREP, 3 - h2, 4 - maf, 5 - effect_range, 6 - pop_id, 7 - strain set
return tuple(parts[0], parts[1], parts[2], parts[3], parts[4], parts[5], parts[6], file)
}
raw_mappings_loco = Channel.fromPath("${sim_dir}/Simulations/gamma/5/Mappings/*_*_*_*_*_ce.192*_lmm-exact_pca.loco.mlma")
// pull out the simulation ID from the file name
.map{ file ->
def parts = file.getBaseName().split('_')
// 1 - NQTL, 2 - SIMREP, 3 - h2, 4 - maf, 5 - effect_range, 6 - pop_id, 7 - strain set
return tuple(parts[0], parts[1], parts[2], parts[3], parts[4], parts[5], parts[6], file)
}
// join the raw mapping channels
raw_mappings_joined = raw_mappings_inbred
.join(raw_mappings_loco, by: [0,1,2,3,4,5,6])
.join(effects_ch, by: [0,1,2,3,4,5,6])
.join(cv_ch, by: [0,1,2,3,4,5,6])
.map{ tuple ->
def (nqtl, simrep, h2, maf, effect_range, pop_id, strain_set, inbred_mapping, loco_mapping, phenotypes, causal_variants) = tuple
return [pop_id, strain_set, maf, nqtl, simrep, h2, effect_range, inbred_mapping, loco_mapping, phenotypes, causal_variants]
}
//raw_mappings_joined.view()
//raw_mappings_inbred.view()
// send the raw mapping file to get_gcta_intervals process
//channel for processed INBRED-PCA mappings - WILL ONLY WORK WITH ON NQTL PARAMETER SIMULATIONS & ONLY PULLS THE INBRED MAPPINGS
//processed_LMM-EXACT-INBRED_PCA_mapping.tsv for CB.192 vs processed_LMM-EXACT-INBRED_mapping.tsv for CE. 192 and 192
//proc_mapping_ch = Channel.fromPath("${sim_dir}/Simulations/gamma/5/Mappings/*processed_LMM-EXACT-INBRED_PCA_mapping.tsv")
// .map{ file ->
// def parts = file.getBaseName().split('_')
// return tuple(parts.take(7).join('_'), file)
// }
//proc_mapping_ch.view()
//genotype matrix input channel
gm_ch = Channel.fromPath(
"${sim_dir}/Genotype_Matrix/ce.192*_Genotype_Matrix.tsv"
)
.map{ file ->
def parts = file.getBaseName().split('_')
return tuple(parts[0], parts[1], parts[2] ,file)
}
//gm_ch.view()
//independent tests input chanel
it_ch = Channel.fromPath(
"${sim_dir}/Genotype_Matrix/ce.192*_total_independent_tests.txt"
)
.map{ file ->
def parts = file.getBaseName().split('_')
return tuple(parts[0], parts[1], parts[2] ,file)
}
// join the genotype matrix channel to the independent tests channel using the pop_id and strain set and MAF
gm_joined = gm_ch
.combine(it_ch, by: [0,1,2])
//gm_joined.view()
// join the genotype matrix channel to the raw mapping channel using the pop_id and strain set and MAF
get_intervals_input = gm_joined
.combine(raw_mappings_joined, by: [0,1,2])
.map{ tuple ->
def (pop_id, panel_id, maf, gm, it, nqtl, simrep, h2, effect_range, inbred_mapping, loco_mapping, phenotypes, causal_variants) = tuple
strain_set = pop_id + '_' + panel_id
return [strain_set, panel_id, nqtl, simrep, h2, "fake_loci_file", gm, effect_range, it, maf, inbred_mapping, loco_mapping, causal_variants, phenotypes]
}
.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("${params.bin_dir}/Find_GCTA_Intervals_LOCO.R")) | get_gcta_intervals
get_gcta_intervals.out.assess_data_inbred_pca
.combine(Channel.fromPath("${params.bin_dir}/Assess_Sim.R")) | assess_sims_INBRED
//get_intervals_input.view()
//join the effects channel to the mapping chanel using the simulation ID
//joined_ch = effects_ch
// .join(proc_mapping_ch, by: 0)
//.join(gm_ch, by: 0)
// .join(cv_ch, by: 0)
//.map{ tuple ->
//def (sim_id, effects_file, mapping_file) = tuple
//return tuple(sim_id, effects_file, mapping_file)
// }
//joined_ch.view()
//pull out simulation parameters from the simulation id
// assess_input_ch = joined_ch
// .map{ tuple ->
// def (sim_id, effects_file, mapping_file, cv_file) = tuple
// def parts = sim_id.split('_')
// 1 - NQTL, 2 - SIMREP, 3 - h2, 4 - maf, 5 - effect, 6 - pop_id, 7 - strain set
// return [parts[5], parts[6], parts[3], parts[0], parts[1], parts[2], parts[4], effects_file, mapping_file, cv_file]
// }
//assess_input_ch.view()
//add the genotype matrix to the channel by joining the assess_input_ch to the gm_ch using the pop_id and strain set
//gm_joined = gm_ch
// .combine(assess_input_ch, by: [0,1,2])
// apply function to meet the input cardinality requirements of the assess_sims process
// .map{ tuple ->
// def (pop_id, panel_id, maf, gm, nqtl, sim_rep, h2, effect_range, phenotypes, mapping_file, var_effects) = tuple
// strain_set = pop_id + '_' + panel_id
// return [strain_set, panel_id, nqtl, sim_rep, h2, maf, effect_range, var_effects, phenotypes, gm, mapping_file, "LMM-EXACT-INBRED_PCA"]
// }
//gm_joined.view()
//gm_joined
// .combine(Channel.fromPath("${params.bin_dir}/Assess_Sim.R")) | assess_sims_INBRED | collectFile(name: "${params.out}/INBRED_PCA_all_sims.tsv")
}