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MaxUlysse 2020-03-11 15:39:36 +01:00
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@ -93,33 +93,33 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
Currently documentation is available for the following systems:
- [AWSBATCH](docs/awsbatch.md)
- [BIGPURPLE](docs/bigpurple.md)
- [BINAC](docs/binac.md)
- [CBE](docs/cbe.md)
- [CCGA_DX](docs/ccga_dx.md)
- [CCGA_MED](docs/ccga_med.md)
- [CFC](docs/cfc.md)
- [CRICK](docs/crick.md)
- [CZBIOHUB_AWS](docs/czbiohub.md)
- [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
- [DENBI_QBIC](docs/denbi_qbic.md)
- [EBC](docs/ebc.md)
- [GENOTOUL](docs/genotoul.md)
- [GENOUEST](docs/genouest.md)
- [GIS](docs/gis.md)
- [GOOGLE](docs/google.md)
- [HEBBE](docs/hebbe.md)
- [KRAKEN](docs/kraken.md)
- [MUNIN](docs/munin.md)
- [PASTEUR](docs/pasteur.md)
- [PHOENIX](docs/phoenix.md)
- [PRINCE](docs/prince.md)
- [SHH](docs/shh.md)
- [UCT_HEX](docs/uct_hex.md)
- [UPPMAX](docs/uppmax.md)
- [UTD_GANYMEDE](docs/utd_ganymede.md)
- [UZH](docs/uzh.md)
* [AWSBATCH](docs/awsbatch.md)
* [BIGPURPLE](docs/bigpurple.md)
* [BINAC](docs/binac.md)
* [CBE](docs/cbe.md)
* [CCGA_DX](docs/ccga_dx.md)
* [CCGA_MED](docs/ccga_med.md)
* [CFC](docs/cfc.md)
* [CRICK](docs/crick.md)
* [CZBIOHUB_AWS](docs/czbiohub.md)
* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
* [DENBI_QBIC](docs/denbi_qbic.md)
* [EBC](docs/ebc.md)
* [GENOTOUL](docs/genotoul.md)
* [GENOUEST](docs/genouest.md)
* [GIS](docs/gis.md)
* [GOOGLE](docs/google.md)
* [HEBBE](docs/hebbe.md)
* [KRAKEN](docs/kraken.md)
* [MUNIN](docs/munin.md)
* [PASTEUR](docs/pasteur.md)
* [PHOENIX](docs/phoenix.md)
* [PRINCE](docs/prince.md)
* [SHH](docs/shh.md)
* [UCT_HEX](docs/uct_hex.md)
* [UPPMAX](docs/uppmax.md)
* [UTD_GANYMEDE](docs/utd_ganymede.md)
* [UZH](docs/uzh.md)
### Uploading to `nf-core/configs`
@ -163,15 +163,15 @@ Note that pipeline-specific configs are not required and should only be added if
Currently documentation is available for the following pipeline within the specific profile:
- ampliseq
- [BINAC](docs/pipeline/ampliseq/binac.md)
- eager
- [SHH](docs/pipeline/eager/shh.md)
- rnafusion
- [MUNIN](docs/pipeline/rnafusion/munin.md)
- sarek
- [MUNIN](docs/pipeline/sarek/munin.md)
- [UPPMAX](docs/pipeline/sarek/uppmax.md)
* ampliseq
* [BINAC](docs/pipeline/ampliseq/binac.md)
* eager
* [SHH](docs/pipeline/eager/shh.md)
* rnafusion
* [MUNIN](docs/pipeline/rnafusion/munin.md)
* sarek
* [MUNIN](docs/pipeline/sarek/munin.md)
* [UPPMAX](docs/pipeline/sarek/uppmax.md)
### Enabling pipeline-specific configs within a pipeline
@ -200,7 +200,7 @@ We will be notified automatically when you have created your pull request, and p
[Fork](https://help.github.com/articles/fork-a-repo/) the [`nf-core/configs`](https://github.com/nf-core/configs/) repository to your own GitHub account.
And add or edit the following files in the local clone of your fork.
- `pipeline/<PIPELINE>.config`
* `pipeline/<PIPELINE>.config`
If not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope
@ -210,18 +210,18 @@ profiles {
}
```
- `conf/pipeline/<PIPELINE>/<PROFILE>.config`
* `conf/pipeline/<PIPELINE>/<PROFILE>.config`
Add the custom configuration file to the `conf/pipeline/<PIPELINE>/` directory.
Make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` to the top of `pipeline/<PIPELINE>.config` and set to reasonable values.
Users will get information on who wrote the pipeline-specific configuration profile then when executing the nf-core pipeline and can report back if there are things missing for example.
- `docs/pipeline/<PIPELINE>/<PROFILE>.md`
* `docs/pipeline/<PIPELINE>/<PROFILE>.md`
Add the documentation file to the `docs/pipeline/<PIPELINE>/` directory.
You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone.
- `README.md`
* `README.md`
Edit this file, and add the new pipeline-specific institutional profile to the list in the section Pipeline specific documentation