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add munin/rnafusion specific docs + markdownlint
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MaxUlysse
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2 changed files with 72 additions and 51 deletions
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README.md
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README.md
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@ -6,19 +6,19 @@ A repository for hosting Nextflow configuration files containing custom paramete
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## Table of contents <!-- omit in toc -->
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* [Using an existing config](#using-an-existing-config)
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* [Configuration and parameters](#configuration-and-parameters)
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* [Offline usage](#offline-usage)
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* [Adding a new config](#adding-a-new-config)
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* [Checking user hostnames](#checking-user-hostnames)
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* [Testing](#testing)
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* [Documentation](#documentation)
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* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
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* [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
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* [Pipeline-specific documentation](#pipeline-specific-documentation)
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* [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
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* [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
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* [Help](#help)
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- [Using an existing config](#using-an-existing-config)
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- [Configuration and parameters](#configuration-and-parameters)
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- [Offline usage](#offline-usage)
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- [Adding a new config](#adding-a-new-config)
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- [Checking user hostnames](#checking-user-hostnames)
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- [Testing](#testing)
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- [Documentation](#documentation)
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- [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
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- [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
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- [Pipeline-specific documentation](#pipeline-specific-documentation)
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- [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
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- [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
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- [Help](#help)
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## Using an existing config
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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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@ -163,13 +163,15 @@ Note that pipeline-specific configs are not required and should only be added if
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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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* 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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@ -198,7 +200,7 @@ We will be notified automatically when you have created your pull request, and p
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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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@ -208,18 +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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19
docs/pipeline/rnafusion/munin.md
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19
docs/pipeline/rnafusion/munin.md
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# nf-core/configs: MUNIN rnafusion specific configuration
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Extra specific configuration for rnafusion pipeline
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## Usage
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To use, run the pipeline with `-profile munin`.
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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.
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Example: `nextflow run nf-core/rnafusion -profile munin`
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## rnafusion specific configurations for MUNIN
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Specific configurations for `MUNIN` has been made for rnafusion.
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* `cpus`, `memory` and `time` max requirements.
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* Paths to specific containers
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* Paths to specific references and indexes
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