incomplete download of pgx-main

pgx-main/tests/simulations/gen_dips.nf

@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-//haps1 = Channel.fromFilePairs(params.in_pgvcf, type: 'file') { file -> file.name.replaceAll(/.vcf.gz|.tbi$/,'') }
-
-haps1 = Channel.fromPath(params.in_hap1, type: 'file')
-haps2 = Channel.fromPath(params.in_hap2, type: 'file') 
-
-//haps2 = Channel.fromFilePairs(params.in_haplo, type: 'file') { file -> file.name.replaceAll(/.vcf.gz|.tbi$/,'') }
-
-haps1
-    .combine(haps2)
-    .set {data}
-//    .println()
-
-
-process make_diplo {
-//   maxForks 10
-//   errorStrategy 'ignore'
-//   tag "${name}" 
-//   label 'big_mem'
-   publishDir params.out_dir, mode: 'copy', overwrite: 'true'
-
-   input:
-      file(vcfs) from data   
-
-   output:	        
-      file("*_diplo.vcf.gz") into diplotypes_ch
-     
-   script:
-    """ 
-    tabix ${vcfs.get(0)}
-    tabix ${vcfs.get(1)}
-    bcftools merge ${vcfs.get(0)} ${vcfs.get(1)} | bgzip -c > ${vcfs.get(0).name.replace(/.vcf.gz/, "")}_${vcfs.get(1).name.replace(/.vcf.gz/, "")}_diplo.vcf.gz
-    """
-
-}

pgx-main/tests/simulations/nextflow.config

@@ -1,32 +0,0 @@
-params {
-  in_hap1 = "/path/to/haplotype_files/*.vcf.gz"
-  in_hap2 = "/path/to/haplotype_files/*.p.vcf.gz"
-  out_dir = "/path/to/output_directory"
-}
-
-
-
-process {
-    withLabel: big_mem {
-        cpus = 8
-        memory = 32.GB
-    }
-}
-
-
-
-
-profiles {
-
-    // For execution on a local machine, no containerization. -- Default
-    standard {
-        process.executor = 'local'
-    }
-
-
-    // For execution on a SLURM scheduler, no containerization.
-    slurm {
-        process.executor = 'slurm'
-        process.queue = 'batch'
-    }
-}

pgx-main/tests/simulations/sim_zygosity.py

@@ -1,32 +0,0 @@
-#!/usr/bin/env python
-
-
-# Script: sim_zygosity.py
-# Author: David Twesigomwe
-# Date modified: 15-Dec-2020
-# Purpose: This script simulates the zygosity of variants after concatenating 2 haplotype VCF files.
-# Usage: python3 sim_zygosity.py in_database.txt > output.txt
-
-import os
-import sys
-
-in_file = sys.argv[1]
-
-f = open (in_file, "r")
-
-
-for line in f:
-    list1 = line.strip().split(";")
-    new_list = []
-    for i in list1:
-        x = i + '~0/1'
-        y = i + '~1/1'
-        if x not in new_list:
-            new_list.append(x)
-            
-        else:
-            new_list = list(map(lambda st: str.replace(st, x, y), new_list))
-
-    print(";".join(new_list))
-
-f.close()