rnastructurome/.nf-core.yml at master · nf-core/rnastructurome · GitHub

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repository_type: pipeline
nf_core_version: 4.1.0
lint:
  # iGenomes support intentionally removed (Ensembl / NCBI / custom genome routes
  # are used instead), so the igenomes config files do not exist.
  files_exist:
    - conf/igenomes.config
    - conf/igenomes_ignored.config
    - .github/workflows/linting_comment.yml
  files_unchanged:
    - .gitignore
    - .github/workflows/linting_comment.yml
    - .github/workflows/linting.yml
    - subworkflows/nf-core/utils_nfcore_pipeline/main.nf
    - assets/email_template.html
    - assets/nf-core-rnastructurome_logo_light.png
    - docs/images/nf-core-rnastructurome_logo_light.png
    - docs/images/nf-core-rnastructurome_logo_dark.png
    - .github/workflows/branch.yml
  # bowtie_all: JSON false parses as Python False, Groovy false parses as string
  # "false" — nf-core string-compares them and flags a mismatch for multi-type params.
  nextflow_config:
    - params.bowtie_all
    - config_defaults:
        - params.bowtie_all
  # ensembl_species_map / ncbi_accessions_map have complex Groovy map defaults
  # that nf-core's config parser cannot evaluate; the params are valid.
  schema_params: false
  # ElementTree namespace syntax (triple-brace SVG NS) is falsely detected as Jinja.
  template_strings:
    - bin/r2dt_colour_svg.py
    - bin/viennarna_colour_svg.py
    - modules/local/r2dt/tests/test_r2dt_colour_svg.py
template:
  org: nf-core
  name: rnastructurome
  description: This pipeline analyses chemical-based high-throughput RNA structure probing data
  author: RNAcentral
  version: 1.0.0
  force: true
  outdir: .
  is_nfcore: true