First speed pass

[ewels]

First couple of quick things from looking over the files, without actually reading the real code...

Please delete these files:

• [x] CODEOWNERS
• [x] samplesheet.transformed.csv
  • Is this some kind of testing data? Needs to go into nf-core/test-datasets if so

Minor changes:

• [x] Markdown render error in links in CITATIONS.md (cutadapt, fastp)
• [x] Please update this to https://nf-co.re/pixelator : https://github.com/PixelgenTechnologies/nf-core-pixelator/blob/ccaabedecb40d7817f728473d94a0bfb2a8fde73/nextflow.config#L261
• [x] Then remove this: https://github.com/PixelgenTechnologies/nf-core-pixelator/blob/ccaabedecb40d7817f728473d94a0bfb2a8fde73/.nf-core.yml#L5-L7

Questions

• [x] What is this file for? Apologies if I missed some docs etc, just glancing at the files right now.

[fbdtemme]

samplesheet.transformed.csv was a temp file that sneaked into git. I have removed the files and fixed the markdown rendering error.

For the homepage you mean: https://github.com/nf-core/pixelator right? nf-core lint complains otherwise.

The create-params-template.py file is used to create this file in ./assets/. It is a template to pass to -params-file but with everthing commented out and descriptions and defaults taken from the pipeline schema. It only includes the pixelator specific options.

It can be handy to copy to your job working dir and start editing when you are in a remote machine and do not want to use the nf-core launch terminal interface.

[ewels]

I have removed the files and fixed the markdown rendering error.

Brilliant, thanks!

For the homepage you mean: https://github.com/nf-core/pixelator right?

Right, sorry. Yes - whatever gets linting to pass without ignoring.

and do not want to use the nf-core launch terminal interface.

Who would not want to use such a wonderful thing?! 😭 ok, fair enough, I see how the YAML file is nice to work with 😅

This looks like it should be fairly generic, it's just rendering from the Nextflow schema file, right? What do you think about breaking it out into a subcommand of nf-core/tools? It could be useful for most Nextflow pipelines I think. That would help to keep the pipeline repo clean and also make the tool available to everyone..

The groups seem to be hardcoded, any reason for that?

[fbdtemme]

A subcommand for nf-core tools would be cool. The groups were hard coded to keep the options limited to the actual pixelator specific flags and thus make the file shorter by not including descriptions and default for all the boilerplate parameters. To make it generic for nf-core/tools we can definitely drop the hard-coded parameter groups without issues.

[ewels]

Great! Do you fancy either making a PR to nf-core/tools, or putting the script into a GitHub gist etc. and opening an issue? Ideally we can get this migrated soon and remove it from the pipeline before release..

[ewels]

make the file shorter by not including descriptions and default for all the boilerplate parameters.

Can maybe do the same thing by ignoring everything that has hidden: true in the schema? 🤔 Not sure if there are any that need to stay unhidden but should not be in the params.yml file though..

[fbdtemme]

Yes, that makes sense. I'll make a PR.

[fbdtemme]

You can find the PR here: https://github.com/nf-core/tools/pull/2362

[ewels]

Just waiting for utils/create-params-template.py to be deleted, then this issue can be closed 👍🏻

[fbdtemme]

Right, forgot about that. It is gone now: https://github.com/PixelgenTechnologies/nf-core-pixelator/commit/e9cbb60d3883c70427f6be002c0507c57b85ac98

[ewels]

Thanks!