Clean up some unnecessary folders and files #5
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FelixAntoineLeSieur
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| @@ -72,8 +75,7 @@ If you wish to contribute a new step, please use the following coding standards: | |||
| 6. Add sanity checks and validation for all relevant parameters. | |||
| 7. Perform local tests to validate that the new code works as expected. | |||
| 8. If applicable, add a new test command in `.github/workflow/ci.yml`. | |||
| 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. | |||
| 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. | |||
| 9. Add a description of the output files if relevant to `docs/output.md`. | |||
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Merci pour le ménage! Je vois dans le fichier que peut-être ce serait bien de changer le nom de la branche sur le point numéro 5. On parle d'ouvrir un pull request sur la branche dev, on devrait plutot dire la branch principale dans notre cas (main je crois).
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Ce serait bien aussi d'ajuster la section "Patch" et remplacer la branche "master" par main.
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Merci pour le ménage! Je vois dans le fichier que peut-être ce serait bien de changer le nom de la branche sur le point numéro 5. On parle d'ouvrir un pull request sur la branche dev, on devrait plutot dire la branch principale dans notre cas (main je crois).
changé 'dev' pour 'main'
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Ce serait bien aussi d'ajuster la section "Patch" et remplacer la branche "master" par main.
oui j'ai changé les 'patch' pour 'fix' ou 'hotfix' et remplacé master par main
docs/usage.md
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| ## Samplesheet input | |||
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| You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below. | |||
| You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a tab-separated file with the first column being the family ID. There are 2 possible format, V1 and V2 (See README for details). V1 includes only the family ID and the sample files as columns, while V2 has the sequencingType as a second column in addition the the familyID and sample files. | |||
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Tu voudras probablement décrire seulement le format V2.
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Peut-etre sera automatiquement fixé avec le rebase.
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j'ai changé plusieurs choses dans le document usage.md, la plupart semble ok à garder, mais pour les choses spécifiques, c'est probablement mieux de garder pour un autre PR
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Also added some caveats to contribution and PR template file Ignored some lint tests for modified or removed files
The mirror seems deprecated and is not consistent with prettier-vsc. Ignored several more lint test for removed files.
Updated the nf-core.yml to ignore related lint test
Removed files related to disabled github actions and email notifications
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Changed wording in CONTRIBUTING.md, updated usage.md, removed the fasta samplesheet Doc: Updated changelog
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Removed .devcontainer and .dockstore. Also added some caveats to contribution and PR template file.
Added a permission to the linting .github workflow to attempt to fix the workflow action.