Add file extension for SnakeMake #3953

nh13 · 2017-12-17T03:28:25Z

Previously a file name was defined for SnakeMake: #1834

Currently, the canonical extension is smk (see this discussion with the author (@johanneskoester) of SnakeMake, and the FAQ).

@johanneskoester

Previously a file name was defined for [SnakeMake[(snakemake-wrappers.readthedocs.io): github-linguist#1834 Currently, the canonical extension is `smk` (see [this discussion](https://groups.google.com/forum/#!topic/Snakemake/segLE-RlV_s) with the author (@johanneskoester) of SnakeMake, and the [FAQ](http://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-enable-syntax-highlighting-in-vim-for-snakefiles)).

lildude · 2018-03-28T17:15:17Z

Sorry about the delay in getting to this PR. Unfortunately, this extension isn't popular enough on GitHub for this PR to be merged. At the moment, the stats are:

Total files found: 911
Unique public user/repos: 113
Unique owners: 95

As per the contributing guidelines at https://github.com/github/linguist/blob/master/CONTRIBUTING.md#adding-an-extension-to-a-language "we prefer that extensions be in use in hundreds of repositories before supporting them in Linguist." This is close, but no cigar.

Accordingly, I'll added the "Pending popularity" label.

johanneskoester · 2018-03-28T18:04:52Z

To clarify, it should be both, Snakefile and .smk be considered the official way to detect Snakemake related files.
Maybe this is a misunderstanding, but it seems like it already works for .smk: https://github.com/snakemake-workflows/rna-seq-star-deseq2/blob/master/rules/align.smk

lildude · 2018-03-29T08:58:11Z

Maybe this is a misunderstanding, but it seems like it already works for .smk: https://github.com/snakemake-workflows/rna-seq-star-deseq2/blob/master/rules/align.smk

That file is currently being detected as Python because you've asked for it to be detected as Python - https://github.com/snakemake-workflows/rna-seq-star-deseq2/blob/master/.gitattributes 😄

johanneskoester · 2018-03-30T07:04:48Z

Ah, I forgot about that. Thanks for the clarification!

johanneskoester · 2018-03-30T07:06:39Z

Ok, but still, you already do this automatically for files called "Snakefile". So, basically it is already in. What stands against also doing it for .smk?

lildude · 2018-03-30T09:37:31Z

Ok, but still, you already do this automatically for files called "Snakefile". So, basically it is already in. What stands against also doing it for .smk?

As I mentioned before, popularity. Snakefile is a defined file that is waaaay more popular than the .smk extension and easily satisfies the "hundreds of repositories" requirement. .smk barely tips over 100 at the moment.

johanneskoester · 2018-03-30T09:41:02Z

Ok, I see, given that criterion, this is of course clear. However, both are for the same tool though (Snakemake). While many people just need a single Snakefile, they add these .smk files for modularization within the same repo. Shouldn't popularity rather be measured via the tool, hence taking the sum of Snakefile and .smk occurrences?

lildude · 2018-03-30T19:44:44Z

Shouldn't popularity rather be measured via the tool, hence taking the sum of Snakefile and .smk occurrences?

Unfortunately not. Peeps can use whatever extension they like with most languages. Just because Python is popular, doesn’t mean we should accept .foobar23 as a Python extension when a few peeps use it.

johanneskoester · 2018-04-03T07:58:58Z

Ok, I understand. We can wait then ;-).

‘smk’ appears to be the accepted file extension for these things. See github-linguist/linguist#3953

pchaigno · 2018-08-04T14:08:59Z

Closing in favor of #4219. We'll monitor the popularity of the extension there.

If you have an improved search query compared to the one used in #4219, please post it here and I'll update #4219.

pchaigno · 2019-09-19T09:40:21Z

The .smk file extension is now popular enough for inclusion (see #4219). @nh13 Do you want me to reopen this pull request or would you prefer to resubmit as a new pull request?

nh13 · 2019-09-19T13:53:24Z

Let’s reopen!

pchaigno · 2019-09-19T14:04:17Z

Ok! You'll need to add and fill in our template for pull requests.

stale · 2019-10-19T14:45:51Z

This pull request has been automatically marked as stale because it has not had recent activity, and will be closed if no further activity occurs. If this pull request was overlooked, forgotten, or should remain open for any other reason, please reply here to call attention to it and remove the stale status. Thank you for your contributions.

nh13 · 2019-10-19T16:43:50Z

I’ll update the pr

stale · 2019-11-18T17:38:52Z

This pull request has been automatically marked as stale because it has not had recent activity, and will be closed if no further activity occurs. If this pull request was overlooked, forgotten, or should remain open for any other reason, please reply here to call attention to it and remove the stale status. Thank you for your contributions.

nh13 · 2019-11-18T20:37:21Z

@johanneskoester do you want to take this one over (in particular the checklist?)

stale · 2019-12-18T21:23:08Z

This pull request has been automatically marked as stale because it has not had recent activity, and will be closed if no further activity occurs. If this pull request was overlooked, forgotten, or should remain open for any other reason, please reply here to call attention to it and remove the stale status. Thank you for your contributions.

johanneskoester · 2019-12-28T20:17:34Z

Description

Checklist:

johanneskoester · 2019-12-28T20:18:53Z

@nh13 here we go. Do you need anything else?

pchaigno · 2020-01-03T08:51:58Z

I have included a real-world usage sample for all extensions added in this PR:
Sample source(s):
https://github.com/snakemake-workflows/rna-seq-kallisto-sleuth
https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling

@johanneskoester @nh13 Could you add one or two files from these repositories to the pull request, under samples/Python/?

johanneskoester · 2020-01-05T23:11:30Z

@nh13 I don't think that I have access to your branch. Can you add one of the smk files from dna-seq-gatk-variant-calling?

nh13 · 2020-01-06T03:14:18Z

Will do when I’m back from vacation in a week or so.

nh13 · 2020-01-10T22:34:22Z

@johanneskoester added:

samples/Python/snakemake-calling.smk
samples/Python/snakemake-mapping.smk

I also added you as a collaborator :)

johanneskoester · 2020-01-10T23:06:40Z

Thanks a lot! I am looking forward to see this automatic highlighting Github and Atom.

pchaigno

Thanks!

@johanneskoester

* Add file extension for SnakeMake Previously a file name was defined for [SnakeMake[(snakemake-wrappers.readthedocs.io): github-linguist#1834 Currently, the canonical extension is `smk` (see [this discussion](https://groups.google.com/forum/#!topic/Snakemake/segLE-RlV_s) with the author (@johanneskoester) of SnakeMake, and the [FAQ](http://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-enable-syntax-highlighting-in-vim-for-snakefiles)). * Adding two Snakemake (smk) example files

@johanneskoester

* add .4dm extensons * no language for the moment * change the source of syntax highlighting for Agda (#4768) * Add interpreters 'csh' and 'tcsh' for language 'Tcsh' (#4760) * Update languages.yml * Create regtest_nmmnest.csh Source: https://github.com/barlage/WRF-kill/blob/master/tools/regtest_nmmnest.csh * Register `.bibtex` as a BibTeX file-extension (#4764) * Register `.dof` as an INI file-extension (#4766) * Register `.epsi` as a PostScript file-extension (#4763) * Add common extensions to Motorola 68k Assembly (#4637) * Add common extensions to Motorola 68k * Revert ACE mode for m68k assembly * Add heuristics for Motorola 68K Assembly * Add SWIG language and `.i` Assembly extension Co-authored-by: John Gardner <gardnerjohng@gmail.com> * Add file extension for SnakeMake (#3953) * Add file extension for SnakeMake Previously a file name was defined for [SnakeMake[(snakemake-wrappers.readthedocs.io): #1834 Currently, the canonical extension is `smk` (see [this discussion](https://groups.google.com/forum/#!topic/Snakemake/segLE-RlV_s) with the author (@johanneskoester) of SnakeMake, and the [FAQ](http://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-enable-syntax-highlighting-in-vim-for-snakefiles)). * Adding two Snakemake (smk) example files * add .4dm extensons * no language for the moment * add lang-4d tmLanguage * link syntax highliting * typo Co-authored-by: Guillaume Brunerie <guillaume.brunerie+github@gmail.com> Co-authored-by: friedc <52925889+friedc@users.noreply.github.com> Co-authored-by: John Gardner <gardnerjohng@gmail.com> Co-authored-by: Iggy Drougge <idrougge@mac.com> Co-authored-by: Nils Homer <nh13@users.noreply.github.com>

nh13 mentioned this pull request Dec 17, 2017

Snakemake files have Python syntax #2745

Closed

lildude added the Pending Popularity label Mar 28, 2018

hobrien added a commit to hobrien/GENEX-FB2 that referenced this pull request May 29, 2018

rename snakefiles

470bee2

‘smk’ appears to be the accepted file extension for these things. See github-linguist/linguist#3953

pchaigno mentioned this pull request Aug 4, 2018

Extension popularity monitoring #4219

Closed

pchaigno closed this Aug 4, 2018

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Adding two Snakemake (smk) example files

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pchaigno approved these changes Jan 11, 2020

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lildude approved these changes Jan 14, 2020

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lildude merged commit 53379ce into github-linguist:master Jan 14, 2020

uniqueg mentioned this pull request Sep 20, 2020

Include Snakemake in descriptor type enumerator ga4gh/tool-registry-service-schemas#156

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SilasK mentioned this pull request Feb 1, 2023

Create independent Snakemake language #6270

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Add file extension for SnakeMake #3953

Add file extension for SnakeMake #3953

nh13 commented Dec 17, 2017 •

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Add file extension for SnakeMake #3953

Add file extension for SnakeMake #3953

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nh13 commented Dec 17, 2017 • edited

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