#
# This is the Snakemake configuration file that specifies paths and 
# and options for the Combined Haplotype Pipeline
#

{
    # py2 is a bit of a hack so that python2 scripts can be called
    # by snakemake (which is written in python3). The value should
    # do whatever is needed to setup a python2 environment and
    # call the python2 interpreter. Depending on your system configuration,
    # this might involve setting the PATH environment variable or
    # just calling python2
    "py2" : "PATH=$HOME/anaconda2/bin:$PATH; python ",

    # Rscript should set environment as appropriate and call Rscript interpreter
    "Rscript" : "PATH=$HOME/anaconda2/bin:$PATH; Rscript ",

    # WASP directory
    "wasp_dir" : "/iblm/netapp/home/gmcvicker/proj/WASP",


    # directory to write all output data files to
    "base_dir" :  "/iblm/netapp/home/gmcvicker/proj/WASP/CHT/output",

    # minimum number of allele-specific reads (combined across individuals)
    # required to perform combined test on a region
    "min_as_count" : "10",

    # location of chromInfo file containing chromosome names and lengths
    # (can be downloaded from UCSC genome browser)
    "chrom_info" : "/iblm/netapp/home/gmcvicker/proj/WASP/examples/example_data/chromInfo.hg19.txt",

    # directory containing impute or VCF SNP files
    "snp_dir" : "/iblm/netapp/home/gmcvicker/proj/WASP/examples/example_data/genotypes",
    # file containing sample identifiers for impute or VCF SNP file
    "snp_samples" : "/iblm/netapp/home/gmcvicker/proj/WASP/examples/example_data/genotypes/YRI_samples.txt",

    # directory containing bowtie2 index
    # one file per chromosome
    "fasta_dir" : "/iblm/netapp/data1/external/GRC37/chroms",

    # text file containing sample identifiers for the subset of
    # samples that are used in study (one per line)
    "samples_file" : "/iblm/netapp/home/gmcvicker/proj/WASP/examples/example_data/H3K27ac/samples.txt",

    # directory containing BAM files
    "bam_dir" : "/iblm/netapp/home/gmcvicker/proj/WASP/examples/example_data/H3K27ac",

    # postfix of BAM files
    "bam_postfix" : ".keep.rmdup.bam"
}