/
test_assess.nf
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/
test_assess.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 $nextflow.version"
println "On QUEST, you can use `module load python/anaconda3.6; source activate /projects/b1059/software/conda_envs/nf20_env`"
exit 1
}
nextflow.enable.dsl=2
// nextflow.enable.dsl=2
date = new Date().format( 'yyyyMMdd' )
params.out = "Analysis_Results-${date}"
params.bin_dir = "${workflow.projectDir}/bin" // this is different for gcp
include {prepare_simulation_files; chrom_eigen_variants_sims; collect_eigen_variants_sims; simulate_effects_loc; simulate_effects_genome; simulate_map_phenotypes; get_gcta_intervals; assess_sims} from './modules/simulations.nf'
workflow{
assess_1 = [
"AB1,AB2",
"AB1,AB2",
"10",
"1",
"0.8",
"0.5",
"gamma",
"/projects/b1059/projects/Ryan/NemaScan_Updates/NemaScan/20231019_asses_test_1/Simulations/gamma/5/Phenotypes/5_2_0.8_0.05_gamma_ce.96.allout15_irrepressible.grosbeak_sims.par",
"/projects/b1059/projects/Ryan/NemaScan_Updates/NemaScan/20231019_asses_test_1/Simulations/gamma/5/Phenotypes/5_1_0.8_0.05_gamma_ce.96.allout15_irrepressible.grosbeak_sims.phen",
"/projects/b1059/projects/Ryan/NemaScan_Updates/NemaScan/20231019_asses_test_1/Genotype_Matrix/ce.96.allout15_irrepressible.grosbeak_0.05_Genotype_Matrix.tsv",
"/projects/b1059/projects/Ryan/NemaScan_Updates/NemaScan/20231019_asses_test_1/Simulations/gamma/5/Mappings/5_1_0.8_0.05_gamma_ce.96.allout15_irrepressible.grosbeak_processed_LMM-EXACT-INBRED_mapping.tsv",
"${params.bin_dir}/Assess_Sim.R"
]
assess_2 = [
"AB1,AB2",
"AB1,AB2",
"10",
"1",
"0.8",
"0.5",
"gamma",
"/projects/b1059/projects/Ryan/NemaScan_Updates/NemaScan/20231019_asses_test_1/Simulations/gamma/5/Phenotypes/5_2_0.8_0.05_gamma_ce.96.allout15_irrepressible.grosbeak_sims.par",
"/projects/b1059/projects/Ryan/NemaScan_Updates/NemaScan/20231019_asses_test_1/Simulations/gamma/5/Phenotypes/5_1_0.8_0.05_gamma_ce.96.allout15_irrepressible.grosbeak_sims.phen",
"/projects/b1059/projects/Ryan/NemaScan_Updates/NemaScan/20231019_asses_test_1/Genotype_Matrix/ce.96.allout15_irrepressible.grosbeak_0.05_Genotype_Matrix.tsv",
"/projects/b1059/projects/Ryan/NemaScan_Updates/NemaScan/20231019_asses_test_1/Simulations/gamma/5/Mappings/5_1_0.8_0.05_gamma_ce.96.allout15_irrepressible.grosbeak_processed_LMM-EXACT-INBRED_mapping.tsv",
"${params.bin_dir}/Assess_Sim.R"
]
Channel.fromList([assess_1, assess_2]) | assess_sims | collectFile(name: "${params.out}/all_sims.tsv") | view
//both = Channel.from(assess_1, assess_2)
//both | assess_sims
// run assess_sims process on both channels
//.collectFile(name: "${params.out}/all_sims.tsv", newLine = true)
}