conflicting advice in usage document
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Description
Description of the bug
In methylseq v4.1.0 noticed something unclear in the documentation. In the main usage guide under Parameters, it states:
“It is mandatory to provide
--fastaalong with--bismark_index/--bwameth_indexparameters.”
However, on the detailed parameter page (https://nf-co.re/methylseq/parameters/), it says:
“If the aligner is Bismark and
bismark_indexis specified, this parameter is ignored.”
That second description is consistent with older releases I’ve used (e.g., v1.6.1), where a FASTA file was never required unless something had changed in Bismark. So I’m unsure whether the requirement in the v4.1.0 usage guide is accurate.
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
Compare the main usage guide's Parameters section with the detailed parameter page at https://nf-co.re/methylseq/parameters/. Check the documented behavior of --fasta with --bismark_index and --bwameth_index, then make the two descriptions consistent and verify that the resulting guidance matches the current workflow behavior.
Written by the indexing model from the issue text.
Assessment
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100