cookiecutter.json

{
    "directory_name": "snakemake-pipeline-general",
    "aligner": [
        "bowtie2",
        "bwa"
    ],
    "skiptrim": [
        false,
        true
    ],
    "trimmer": [
        "trimmomatic",
        "fastp"
    ],
    "nodes": 1,
    "threads": 4,
    "mem": 32,
    "pe_adapter": "path/to/PE/adapter",
    "se_adapter": "path/to/SE/adapter",
    "fastp": "-g is suggested to handle poly-G issue on new sequencer",
    "bowtie2_index": "path/to/bowtie2/index",
    "bowtie2": "",
    "bwa_index": "path/to/bwa/index",
    "bwa_mem": "",
    "skipfilter": [
        true,
        false
    ],
    "genome_fai": "path/to/genome/fai",
    "bamCoverage_pe": "--extendReads -bs 1 --normalizeUsing RPKM",
    "bamCoverage_se": "--extendReads 200 -bs 1 --normalizeUsing RPKM",
    "blacklist": "path/to/blacklist",
    "transcriptome": "GTF or BED gene/transcript annotation file",
    "_copy_without_render": [
        "*.smk",
        "*Snakefile"
    ],
    "aspera_private_key": ""
}