Adding Superlinter as Github action

bio-raum / FooDMe2

A nextflow pipeline for the identification of species from mixed samples based on mitochondrial amplicons

https://bio-raum.github.io/FooDMe2/

GNU General Public License v3.0

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Adding Superlinter as Github action #3

Closed gregdenay closed 6 months ago

gregdenay commented 6 months ago

Replaces Groovy-linter with Superlinter to include all other code:

Python
YAML/JSON
R
Markdown
Bash
Perl
Groovy

Other languages can be added in the YAML action file.

Fixed Markdown linting Python linter is going crazy over the snakemakes statements, this will be fixed progressively in #2 Still one Groovy Error /github/workspace/subworkflows/illumina_workflow/main.nf: 45 This code cannot be reached DeadCode

marchoeppner commented 6 months ago

Good idea - I think the remaining error should be simple enough to fix down the road.