conf.py

# Module directory
job_modules = "jobs/modules/"

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

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

# Job scripts directory
job_scripts = "jobs/scripts/"

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

# list of resources that can be specified per job (step) in
# the workflow and corresponding Pegasus profile info
resources = {
    "walltime": {
        "namespace": "globus",
        "key": "maxwalltime"
    },
    "memory": {
        "namespace": "condor",
        "key": "request_memory"
    },
    "cores": {
        "namespace": "pegasus",
        "key": "cores"
    }
}

# Defines the types of input / output arguments
# argument -> Any non file argument
# file -> Any file argument that isn't redirected
# stdout -> Any file argument that is redirected from stdout
# stderr -> Any file argument that is redirected from stderr
argument_types = {
    "argument": ["argument"],
    "file": ["file", "stdout", "stderr"]
]

# param keys
param_keys = {
    "required": ["arguments"],
    "optional": resources.keys()
}

# 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"]
    }
}