Improve citations for GATK4 modules
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Description
Have you checked the docs?
Description of the bug
The current citation used by most (did not check all of them) gatk4 modules is a reference to a poster abstract.
However, the gatk docs do not list this reference and seem to recommend different citations for different use cases (e.g. joint calling).
Might be worth updating these?
It would need to be decided which reference to use for which module though, or if it's more pragmatic to stick to a single reference (e.g. the top one recommended by the docs) as to not pollute things like the multiqc output with numerous different gatk citations.
Command used and terminal output
Relevant files
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System information
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Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing the linked GATK citation guidance and the nf-core modules documentation, then audit the GATK4 modules to identify their current citation metadata. Determine whether citations should vary by module or use one standard reference. Done means the chosen citations are consistently applied to the relevant GATK4 modules and their generated citation output is correct.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, documentation
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100