removed pgx-main

pgx-main/tests/config/nat2.config

@@ -1,90 +0,0 @@
-
-
-
-params {
-    gene = "nat2"
-}
-
-
-process {
-
-    // ALL PROCESSES
-    cache = true
-    stageInMode = 'symlink'
-    stageOutMode = 'rsync'
-   // scratch = "$HOME/tmp"  // clean this regularly
-
-    // Containers
-
-    // Singularity
-
-//    withLabel: phase {
-//    singularity.enabled	= false
-    //container = "$PWD/containers/whatshap.sif" // this can be generated from docker://pacificbiosciences/whatshap
-//    }
-
-    withName: call_snvs1 {
-    singularity.enabled = true
-    container = "$PWD/containers/stellarpgx-dev.sif"
-    }
-
-    withName: call_snvs2 {
-    singularity.enabled	= true
-    container = "$PWD/containers/stellarpgx-dev.sif"
-    }
-
-    withName: call_sv_del {
-    singularity.enabled	= true
-    container = "$PWD/containers/stellarpgx-dev.sif"
-    }
-
-    withName: call_sv_dup {
-    singularity.enabled	= true
-    container = "$PWD/containers/stellarpgx-dev.sif"
-    }
-
-    withName: get_depth {
-    singularity.enabled	= true
-    container = "$PWD/containers/stellarpgx-dev.sif"
-    }
-
-    withName: format_snvs {
-    singularity.enabled	= true
-    container = "$PWD/containers/stellarpgx-dev.sif"
-    }
-
-    withName: get_core_var {
-    singularity.enabled	= true
-    container = "$PWD/containers/stellarpgx-dev.sif"
-    }
-
-    withName: analyse_1 {
-    singularity.enabled = true
-    container = "$PWD/containers/stellarpgx-dev.sif"
-    }
-
-    withName: analyse_2 {
-    singularity.enabled = true
-    container = "$PWD/containers/stellarpgx-dev.sif"
-    }
-
-    withName: analyse_3 {
-    singularity.enabled = true
-    container = "$PWD/containers/stellarpgx-dev.sif"
-    }
-
-    withName: analyse_4 {
-    singularity.enabled = true
-    container = "$PWD/containers/stellarpgx-dev.sif"
-    }
-
-    withName: call_stars {
-    singularity.enabled = true
-    container = "$PWD/containers/stellarpgx-dev.sif"
-    }
-
-    
-    // Docker
-    // container = "twesigomwedavid/stellarpgx-dev:latest" // Note that this Docker build needs to be pulled from Do
-
-}

pgx-main/tests/config/test.config

@@ -1,23 +0,0 @@
-
-
-params {
-// User-defined parameters
-
-   // reference genome
-   ref_file = "$PWD/tests/reference/hg38/chr22_hg38.fasta"
-
-
-   // BAM/CRAM file(s) and respective indexes 
-   in_bam = "$PWD/tests/samples/hg38/HG03130*{bam,bai}" 
-
-
-   // Output directoy (Default is $PWD/results)
-   out_dir = "$PWD/results"
-
-
-   // DO NOT modify these lines  
-   gene = "cyp2d6"
-   res_init = "$PWD/tests/resources"
-
-}
-

pgx-main/tests/reference/hg38/chr22_hg38.fasta.fai

@@ -1 +0,0 @@
-chr22	50818468	7	70	71

pgx-main/tests/resources/cyp2d6/res_hg38/test3.bed

@@ -1,11 +0,0 @@
-chr22	42126300	42126800
-chr22	42127750	42130000
-chr22	42126000	42137500
-chr22	42149880	42155020
-chr22	42139000	42142455
-chr22	42142465	42144575
-chr22	42139500	42140600
-chr22	42140600	42142500
-chr22	42149883	42155000
-chr22	42140600	42143600
-chr22	42143600	42144575

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()