build_default_tool_binary_list: Build default tools binaries config

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Build default tools binaries config

Description

Build default tools binaries config

Usage

build_default_tool_binary_list(
  binaries = list(bin_fastqc =
    "/lustre/scratch/scratch/regmova/tools/FastQC/bin/fastqc", bin_skewer =
    "/lustre/scratch/scratch/regmova/tools/skewer/skewer", bin_fastqc =
    "/lustre/scratch/scratch/regmova/tools/FastQC/bin/fastqc", bin_bcftools =
    "/lustre/scratch/scratch/regmova/tools/bcftools/bcftools", bin_bgzip =
    "/lustre/scratch/scratch/regmova/tools/htslib/bin/bgzip", bin_tabix =
    "/lustre/scratch/scratch/regmova/tools/htslib/bin/tabix", bin_htsfile =
    "/lustre/scratch/scratch/regmova/tools/htslib/bin/htsfile", 
     bin_nextflow =
    "/lustre/home/regmova/bin/nextflow", bin_aasuite =
    "/lustre/scratch/scratch/regmova/tools/AmpliconSuite-pipeline/singularity/run_paa_singularity.py",
    bin_bwa = "/lustre/scratch/scratch/regmova/tools/bwa/bwa", bin_shapeit =
    "/lustre/scratch/scratch/regmova/tools/shapeit4/bin/shapeit", bin_allele_counter =
    "/lustre/scratch/scratch/regmova/tools/alleleCount/bin/alleleCounter", bin_strelka =
    list(somatic =
    "/lustre/scratch/scratch/regmova/tools/strelka-2.9.10/bin/configureStrelkaSomaticWorkflow.py",
    
         germline =
    "/lustre/scratch/scratch/regmova/tools/strelka-2.9.10/bin/configureStrelkaGermlineWorkflow.py"),
    bin_ucsc = list(bigBedToBed =
    "/lustre/scratch/scratch/regmova/tools/OtherTools/bigBedToBed", bedToBigBed =
    "/lustre/scratch/scratch/regmova/tools/OtherTools/bedToBigBed", liftOver =
    "/lustre/scratch/scratch/regmova/tools/OtherTools/liftOver"), bin_sshpass =
    "/lustre/scratch/scratch/regmova/tools/sshpass/sshpass", bin_vep =
    "/lustre/scratch/scratch/regmova/tools/ensembl-vep/vep", bin_manta =
    "/lustre/scratch/scratch/regmova/tools/manta-1.6.0/bin/configManta.py", 
    
    bin_ichor_pon =
    "/lustre/scratch/scratch/regmova/tools/ichorCNA/scripts/createPanelOfNormals.R",
    bin_ichor = "/lustre/scratch/scratch/regmova/tools/ichorCNA/scripts/runIchorCNA.R",
    bin_samtools = "/lustre/scratch/scratch/regmova/tools/samtools/samtools", bin_gatk =
    "/lustre/scratch/scratch/regmova/tools/gatk/gatk", bin_readcount =
    "/lustre/scratch/scratch/regmova/tools/hmmcopy_utils/bin/readCounter", bin_ciri =
    "/lustre/scratch/scratch/regmova/tools/CIRI/CIRI_Full_v2.1.1.jar", bin_picard =
    "/lustre/scratch/scratch/regmova/tools/picard/build/libs/picard.jar", 
    
    bin_samtools = "/lustre/scratch/scratch/regmova/tools/samtools/samtools", bin_picard
    = "/lustre/scratch/scratch/regmova/tools/picard/build/libs/picard.jar", bin_bedtools
    = "/lustre/scratch/scratch/regmova/tools/bedtools2/bin/bedtools", bin_ciri_quant =
    "/lustre/scratch/scratch/regmova/tools/CIRIquant/bin/CIRIquant")
)

Arguments

binaries

List with tool_names and paths

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.