nf-core / nf-core/website

Broken link in documentation: [404] Page not found: https://nf-co.re/sarek/3.10.0/docs/output/

Open Beginner friendly
#4,401 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

bug
Dominant language
MDX
Stars
98
Forks
298
Avg merge
14h 38m
Merged PRs (30d)
38

Description

Hi,

Thanks very much for this pipeline and the great documentation!

Just reporting a broken link in the documentation.

Link found here:
https://nf-co.re/sarek/3.10.0/docs/output/#variant-calling, at the end of the SNVs and small indels (broken link = https://nf-co.re/sarek/3.10.0/docs/output/usage#which-tool )

Variant Calling
The results regarding variant calling are collected in {outdir}/variant_calling/. If some results from a variant caller do not appear here, please check out the --tools section in the parameter [documentation](https://nf-co.re/sarek/latest/parameters).

(Recalibrated) CRAM files can used as an input to start the variant calling.

SNVs and small indels
For single nucleotide variants (SNVs) and small indels, multiple tools are available for normal (germline), tumor-only, and tumor-normal (somatic) paired data. For a list of the appropriate tool(s) for the data and sequencing type at hand, please check [here](https://nf-co.re/sarek/3.10.0/docs/output/usage#which-tool).

Thanks.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start at the Sarek 3.10.0 output documentation page and inspect the SNVs and small indels section, especially the link ending in /docs/output/usage#which-tool. Update the broken destination to the correct documentation page, then verify that the link resolves and points to the intended tool-selection guidance.

Written by the indexing model from the issue text.

Assessment

Domain
documentation
Issue type
Documentation
Difficulty
1/5
Estimated time
Under an hour
Activity status
Active
Clarity
Clearly specified
Newbie friendliness
85/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.