# Module directory
job_modules = "jobs/modules/"

# Job params directory
job_params = "jobs/params/"

# Job wrappers directory
job_wrappers = "jobs/wrappers/"

# File extensions
file_extensions = {
    "genome_index": ["fa", "fna"],
    "fastq": ["fastq", "fastq.gz"],
    "sam": ["sam"],
    "bam": ["bam"],
    "bed": ["bed", "narrowPeak", "broadPeak"],
    "bwa_genome": ["amb", "ann", "bwt", "pac", "sac"],
    "bowtie2_genome": ["1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"]
}

# param keys
param_keys = {
    "required": ["arguments"],
    "optional": ["walltime", "memory"]
}

# workflow order
workflow = ["align", "remove_duplicates", "peak_calling"]

# genome info
genomes = {
    "bwa": {
        "base_file": file_extensions["genome_index"],
        "additional_files": file_extensions["bwa_genome"]
    },
    "bowtie2": {
        "base_file": file_extensions["genome_index"],
        "additional_files": file_extensions["bowtie2_genome"]
    }
}