cookiecutter.json

{
    "project_name": "newproject",
    "projects_base": "projects",
    "data_type": "rnaseq",
    "rnaseq_samples_dir": "",
    "rnaseq_samples": "",
    "fastq_suffix": "fastq.gz",
    "paired_end_read": "yes",
    "read1_identifier": "_1",
    "read2_identifier": "{{ cookiecutter.read1_identifier|replace('1', '2') }}",
    "ensembl_version": "115",
    "msigdb_version": "2025.1",
    "number_threads_per_sample": 8,
    "number_total_threads": 32,
    "sargasso": "no",
    "strategy": "conservative",
    "species": "mouse rat human",
    "star_version": "2.7.11b",
    "bowtie2_version": "2.4.4",
    "salmon_version": "1.10.0",
    "featurecounts_version": "2.1.1",
    "picard_version": "2.25.6",
    "fastqc_version": "0.12.0",
    "qSVA": "no",
    "virtualenv_home": ".virtualenvs",
    "human_assembly": "GRCh38",
    "mouse_assembly": "GRCm39",
    "rat_assembly": "mRatBN7.2",
    "gtf_files": {
        "mouse": "Mus_musculus.{{ cookiecutter.mouse_assembly }}.{{ cookiecutter.ensembl_version }}.gtf",
        "human": "Homo_sapiens.{{ cookiecutter.human_assembly }}.{{ cookiecutter.ensembl_version }}.gtf",
        "rat": "Rattus_norvegicus.{{ cookiecutter.rat_assembly }}.{{ cookiecutter.ensembl_version }}.gtf"
    },
    "rff_files": {
        "mouse": "Mus_musculus.{{ cookiecutter.mouse_assembly }}.{{ cookiecutter.ensembl_version }}.rff",
        "human": "Homo_sapiens.{{ cookiecutter.human_assembly }}.{{ cookiecutter.ensembl_version }}.rff",
        "rat": "Rattus_norvegicus.{{ cookiecutter.rat_assembly }}.{{ cookiecutter.ensembl_version }}.rff"
    },
    "assembly_names": {
        "mouse": "primary_assembly",
        "human": "primary_assembly",
        "rat": "toplevel"
    }
}