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@ -93,33 +93,33 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
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Currently documentation is available for the following systems:
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- [AWSBATCH](docs/awsbatch.md)
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- [BIGPURPLE](docs/bigpurple.md)
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- [BINAC](docs/binac.md)
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- [CBE](docs/cbe.md)
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- [CCGA_DX](docs/ccga_dx.md)
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- [CCGA_MED](docs/ccga_med.md)
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- [CFC](docs/cfc.md)
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- [CRICK](docs/crick.md)
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- [CZBIOHUB_AWS](docs/czbiohub.md)
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- [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
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- [DENBI_QBIC](docs/denbi_qbic.md)
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- [EBC](docs/ebc.md)
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- [GENOTOUL](docs/genotoul.md)
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- [GENOUEST](docs/genouest.md)
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- [GIS](docs/gis.md)
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- [GOOGLE](docs/google.md)
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- [HEBBE](docs/hebbe.md)
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- [KRAKEN](docs/kraken.md)
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- [MUNIN](docs/munin.md)
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- [PASTEUR](docs/pasteur.md)
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- [PHOENIX](docs/phoenix.md)
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- [PRINCE](docs/prince.md)
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- [SHH](docs/shh.md)
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- [UCT_HEX](docs/uct_hex.md)
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- [UPPMAX](docs/uppmax.md)
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- [UTD_GANYMEDE](docs/utd_ganymede.md)
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- [UZH](docs/uzh.md)
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* [AWSBATCH](docs/awsbatch.md)
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* [BIGPURPLE](docs/bigpurple.md)
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* [BINAC](docs/binac.md)
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* [CBE](docs/cbe.md)
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* [CCGA_DX](docs/ccga_dx.md)
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* [CCGA_MED](docs/ccga_med.md)
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* [CFC](docs/cfc.md)
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* [CRICK](docs/crick.md)
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* [CZBIOHUB_AWS](docs/czbiohub.md)
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* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
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* [DENBI_QBIC](docs/denbi_qbic.md)
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* [EBC](docs/ebc.md)
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* [GENOTOUL](docs/genotoul.md)
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* [GENOUEST](docs/genouest.md)
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* [GIS](docs/gis.md)
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* [GOOGLE](docs/google.md)
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* [HEBBE](docs/hebbe.md)
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* [KRAKEN](docs/kraken.md)
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* [MUNIN](docs/munin.md)
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* [PASTEUR](docs/pasteur.md)
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* [PHOENIX](docs/phoenix.md)
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* [PRINCE](docs/prince.md)
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* [SHH](docs/shh.md)
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* [UCT_HEX](docs/uct_hex.md)
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* [UPPMAX](docs/uppmax.md)
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* [UTD_GANYMEDE](docs/utd_ganymede.md)
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* [UZH](docs/uzh.md)
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### Uploading to `nf-core/configs`
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Currently documentation is available for the following pipeline within the specific profile:
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- ampliseq
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- [BINAC](docs/pipeline/ampliseq/binac.md)
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- eager
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- [SHH](docs/pipeline/eager/shh.md)
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- rnafusion
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- [MUNIN](docs/pipeline/rnafusion/munin.md)
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- sarek
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- [MUNIN](docs/pipeline/sarek/munin.md)
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- [UPPMAX](docs/pipeline/sarek/uppmax.md)
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* ampliseq
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* [BINAC](docs/pipeline/ampliseq/binac.md)
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* eager
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* [SHH](docs/pipeline/eager/shh.md)
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* rnafusion
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* [MUNIN](docs/pipeline/rnafusion/munin.md)
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* sarek
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* [MUNIN](docs/pipeline/sarek/munin.md)
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* [UPPMAX](docs/pipeline/sarek/uppmax.md)
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### Enabling pipeline-specific configs within a pipeline
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[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.
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And add or edit the following files in the local clone of your fork.
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- `pipeline/<PIPELINE>.config`
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* `pipeline/<PIPELINE>.config`
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If not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope
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@ -210,18 +210,18 @@ profiles {
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}
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```
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- `conf/pipeline/<PIPELINE>/<PROFILE>.config`
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* `conf/pipeline/<PIPELINE>/<PROFILE>.config`
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Add the custom configuration file to the `conf/pipeline/<PIPELINE>/` directory.
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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.
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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.
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- `docs/pipeline/<PIPELINE>/<PROFILE>.md`
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* `docs/pipeline/<PIPELINE>/<PROFILE>.md`
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Add the documentation file to the `docs/pipeline/<PIPELINE>/` directory.
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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.
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- `README.md`
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* `README.md`
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Edit this file, and add the new pipeline-specific institutional profile to the list in the section Pipeline specific documentation
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