new module: fairbioheaders (combine, verify, convert, validate) #13491

Is there an existing module for this?

• I have searched for the existing module

Is there an open PR for this?

• I have searched for existing PRs

Is there an open issue for this?

• I have searched for existing issues

Further Information

fair-bioheaders (Bioconda fair-bioheaders, CLI bioheaders, MPL-2.0, bio.tools fair-bioheaders) reads and writes FAIR-bioHeaders provenance headers: FHR for genome FASTA and GFA, FHP for protein FASTA and FHGFF3 for GFF3 (paper: doi:10.1093/bib/bbae122). The header records provenance such as taxon, authors, version and masking state, and a checksum of the file.

Planned modules, one PR each:

• fairbioheaders/combine: attach metadata to a FASTA, GFA or GFF3 file and record its checksum
• fairbioheaders/verify: check a headed file's header against its schema and its checksum
• fairbioheaders/convert: write a header as JSON, YAML, JSON-LD or HTML, e.g. a sidecar YAML file
• fairbioheaders/validate: validate standalone metadata before a run

Motivating use: nf-core/genomeassembler#250 adds an optional FHR export of assembly outputs (tracked in nf-core/genomeassembler#242), and the maintainer asked for it to use nf-core modules.

Are you going to work on this?

• If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module

Software requirements (conda)

---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
  - conda-forge
  - bioconda
dependencies:
  - bioconda::fair-bioheaders=0.8.5