tools: Images in output.md not rendered when converted to html
The template contains a process called output_documentation that converts the pipeline’s output documentation i.e. docs/output.md to html format in order to be stored with the results. However, if there are images embedded or linked in this document then these wont be rendered properly and so the links just appear to be broken. Im wondering whether using absolute instead of relative paths will solve this… 🤔
About this issue
- Original URL
- State: closed
- Created 5 years ago
- Comments: 15 (15 by maintainers)
haha, is that it? That the images weren’t being staged in the work directory? Of course! Nothing to do with the script itself - no wonder I couldn’t replicate the problem 🤦
Nice work @svarona!
I guess the only real problem is that
output.mdwill change over time and so we will need a more dynamic way of referring to the docs for that particular pipeline release. At the moment, thats not a problem because it will be generated from the docs at the time.Looks like you can use tag (release) names directly in the GitHub URLs too, so we don’t have to worry about fetching commit hashes: https://github.com/nf-core/atacseq/blob/1.0.0/docs/output.md
Yes, the same question passed through my mind to be honest. It is a relic of the early days of the NGI pipelines really. But I think that is probably is still useful in our use case - specifically when pipeline results are delivered to a user who has no knowledge (or interest) of the pipeline that generated those results.
I guess we could just link to the online docs though. Maybe a shortcut file?? Remember those? 😆
output_file_documentation.url:To be honest, it wouldn’t be a terrible idea to rewrite this functionality. I don’t love that it’s done with an R script, as it means that every pipeline has to have R in the container. Could be better to have it in a Python script, as we’re using conda…