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add munin/rnafusion specific docs + markdownlint

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MaxUlysse 2020-03-11 14:23:23 +01:00
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README.md
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@ -6,19 +6,19 @@ A repository for hosting Nextflow configuration files containing custom paramete
## Table of contents <!-- omit in toc --> ## Table of contents <!-- omit in toc -->
* [Using an existing config](#using-an-existing-config) - [Using an existing config](#using-an-existing-config)
* [Configuration and parameters](#configuration-and-parameters) - [Configuration and parameters](#configuration-and-parameters)
* [Offline usage](#offline-usage) - [Offline usage](#offline-usage)
* [Adding a new config](#adding-a-new-config) - [Adding a new config](#adding-a-new-config)
* [Checking user hostnames](#checking-user-hostnames) - [Checking user hostnames](#checking-user-hostnames)
* [Testing](#testing) - [Testing](#testing)
* [Documentation](#documentation) - [Documentation](#documentation)
* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs) - [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
* [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config) - [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
* [Pipeline-specific documentation](#pipeline-specific-documentation) - [Pipeline-specific documentation](#pipeline-specific-documentation)
* [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline) - [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
* [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files) - [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
* [Help](#help) - [Help](#help)
## Using an existing config ## Using an existing config
@ -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: Currently documentation is available for the following systems:
* [AWSBATCH](docs/awsbatch.md) - [AWSBATCH](docs/awsbatch.md)
* [BIGPURPLE](docs/bigpurple.md) - [BIGPURPLE](docs/bigpurple.md)
* [BINAC](docs/binac.md) - [BINAC](docs/binac.md)
* [CBE](docs/cbe.md) - [CBE](docs/cbe.md)
* [CCGA_DX](docs/ccga_dx.md) - [CCGA_DX](docs/ccga_dx.md)
* [CCGA_MED](docs/ccga_med.md) - [CCGA_MED](docs/ccga_med.md)
* [CFC](docs/cfc.md) - [CFC](docs/cfc.md)
* [CRICK](docs/crick.md) - [CRICK](docs/crick.md)
* [CZBIOHUB_AWS](docs/czbiohub.md) - [CZBIOHUB_AWS](docs/czbiohub.md)
* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md) - [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
* [DENBI_QBIC](docs/denbi_qbic.md) - [DENBI_QBIC](docs/denbi_qbic.md)
* [EBC](docs/ebc.md) - [EBC](docs/ebc.md)
* [GENOTOUL](docs/genotoul.md) - [GENOTOUL](docs/genotoul.md)
* [GENOUEST](docs/genouest.md) - [GENOUEST](docs/genouest.md)
* [GIS](docs/gis.md) - [GIS](docs/gis.md)
* [GOOGLE](docs/google.md) - [GOOGLE](docs/google.md)
* [HEBBE](docs/hebbe.md) - [HEBBE](docs/hebbe.md)
* [KRAKEN](docs/kraken.md) - [KRAKEN](docs/kraken.md)
* [MUNIN](docs/munin.md) - [MUNIN](docs/munin.md)
* [PASTEUR](docs/pasteur.md) - [PASTEUR](docs/pasteur.md)
* [PHOENIX](docs/phoenix.md) - [PHOENIX](docs/phoenix.md)
* [PRINCE](docs/prince.md) - [PRINCE](docs/prince.md)
* [SHH](docs/shh.md) - [SHH](docs/shh.md)
* [UCT_HEX](docs/uct_hex.md) - [UCT_HEX](docs/uct_hex.md)
* [UPPMAX](docs/uppmax.md) - [UPPMAX](docs/uppmax.md)
* [UTD_GANYMEDE](docs/utd_ganymede.md) - [UTD_GANYMEDE](docs/utd_ganymede.md)
* [UZH](docs/uzh.md) - [UZH](docs/uzh.md)
### Uploading to `nf-core/configs` ### Uploading to `nf-core/configs`
@ -163,13 +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: Currently documentation is available for the following pipeline within the specific profile:
* ampliseq - ampliseq
* [BINAC](docs/pipeline/ampliseq/binac.md) - [BINAC](docs/pipeline/ampliseq/binac.md)
* eager - eager
* [SHH](docs/pipeline/eager/shh.md) - [SHH](docs/pipeline/eager/shh.md)
* sarek - rnafusion
* [MUNIN](docs/pipeline/sarek/munin.md) - [MUNIN](docs/pipeline/rnafusion/munin.md)
* [UPPMAX](docs/pipeline/sarek/uppmax.md) - sarek
- [MUNIN](docs/pipeline/sarek/munin.md)
- [UPPMAX](docs/pipeline/sarek/uppmax.md)
### Enabling pipeline-specific configs within a pipeline ### Enabling pipeline-specific configs within a pipeline
@ -198,7 +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. [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. 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 If not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope
@ -208,18 +210,18 @@ profiles {
} }
``` ```
* `conf/pipeline/<PIPELINE>/<PROFILE>.config` - `conf/pipeline/<PIPELINE>/<PROFILE>.config`
Add the custom configuration file to the `conf/pipeline/<PIPELINE>/` directory. 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. 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. 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. 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. 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 Edit this file, and add the new pipeline-specific institutional profile to the list in the section Pipeline specific documentation

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docs/pipeline/rnafusion/munin.md Normal file
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@ -0,0 +1,19 @@
# nf-core/configs: MUNIN rnafusion specific configuration
Extra specific configuration for rnafusion pipeline
## Usage
To use, run the pipeline with `-profile munin`.
This will download and launch the rnafusion specific [`munin.config`](../../../conf/pipeline/rnafusion/munin.config) which has been pre-configured with a setup suitable for the `MUNIN` cluster.
Example: `nextflow run nf-core/rnafusion -profile munin`
## rnafusion specific configurations for MUNIN
Specific configurations for `MUNIN` has been made for rnafusion.
* `cpus`, `memory` and `time` max requirements.
* Paths to specific containers
* Paths to specific references and indexes