chbk

Default themes maintenance

3

### Description - Bug fixes: - Fixes comment punctuation in CSS - Adds a rule to highlight functions in Sass and Less differently than vanilla CSS - Highlighting legibility improvements:...

Implement naming conventions in Python grammar

6

### Description of the Change This is a rewrite of the Tree-sitter grammar to implement [naming conventions](https://github.com/atom/flight-manual.atom.io/pull/564) for syntax scopes. ### Benefits - Many new scopes added to make the...

Detect placeholders in pre-formatted strings

3

I would love it if Tree-sitter handled placeholders in regular strings: ```python 'My name is %12s' % 'Slim Shady' 'My name is %(name)12s' % {'name': 'Slim Shady'} 'My name is...

Problem using hyphens in group names

1

`read.delim` is used [here](https://github.com/nf-core/atacseq/blob/1b3a832db5a53c92c2c89a4d6d79455e860461ad/bin/featurecounts_deseq2.r#L62). That function implicitly replaces hyphens with periods. Group names get changed which leads to incorrect merging.

Some samples aren't processed

2

In the MultiQC report, only one of the samples appears in the following sections: - MERGED LIB: PICARD - MERGED LIB: deepTools: Read Distribution Profile after Annotation - MERGED LIB:...

Bug report for an edge case that I encountered. When the fasta option is given a glob, for example `--fasta 'genome/*'`, the `bwa_base` variable is set to `*` at [line...

Channel used twice as an input

4

Bug report for this error: ``` Channel `ch_gene_bed` has been used twice as an input by process `MERGED_LIB_PLOTPROFILE` and process `MAKE_TSS_BED` -- Check script 'nf-core/atacseq/main.nf' at line: 1023 ``` -...

Naming conventions for syntax scopes

20

## Motivations for this PR The lack of documentation on syntax scopes has been an [issue](https://github.com/atom/atom/issues/8430) for many years and still hinders the progress of contributors who wish to create...

Implement naming conventions in Ruby grammar

1

### Description of the Change This is a rewrite of the Tree-sitter grammar to implement [naming conventions](https://github.com/atom/flight-manual.atom.io/pull/564) for syntax scopes. ### Benefits - Many new scopes added to make the...

Implement naming conventions in CSS grammar

3

### Description of the Change This is a rewrite of the Tree-sitter grammar to implement [naming conventions](https://github.com/atom/flight-manual.atom.io/pull/564) for syntax scopes. Currently, Atom uses the TextMate grammar because the Tree-sitter grammar...