conf.py 975 Bytes
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# Module directory
job_modules = "jobs/modules/"

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

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

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

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