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update docs

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MaxUlysse 2019-11-20 15:32:35 +01:00
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6
README.md
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@ -12,6 +12,10 @@ A repository for hosting nextflow config files containing custom parameters requ
* [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)
* [Pipeline Specific Documentation](#pipeline-specific-documentation)
* [Enabling the specific configs within a specific pipeline](#enabling-the-specific-configs-within-a-specific-pipeline)
* [Create the specific `nf-core/configs` for the pipeline](#create-the-specific-nf-coreconfigs-for-the-pipeline)
* [Help](#help) * [Help](#help)
## Using an existing config ## Using an existing config
@ -128,7 +132,7 @@ Currently documentation is available for the following pipelines within the spec
* sarek * sarek
* [MUNIN](docs/pipeline/sarek/munin.md) * [MUNIN](docs/pipeline/sarek/munin.md)
### Enabling the specific configs within a specific PIPELINE ### Enabling the specific configs within a specific pipeline
> This has to be done on a fork of the `nf-core/<PIPELINE>` repository. > This has to be done on a fork of the `nf-core/<PIPELINE>` repository.

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docs/pipeline/sarek/munin.md
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@ -10,12 +10,13 @@ This will download and launch the [`munin.config`](../conf/pipeline/sarek/munin.
Example: `nextflow run nf-core/sarek -profile munin` Example: `nextflow run nf-core/sarek -profile munin`
## Sarek specific configurations for Munin ## Sarek specific configurations for MUNIN
Specific configurations for Munin has been made for sarek. Specific configurations for MUNIN has been made for sarek.
* Params `annotation_cache` set to `true`
* Path to `snpEff_cache`: `/data1/cache/snpEff/` * Path to `snpEff_cache`: `/data1/cache/snpEff/`
* Path to `vep_cache`: `/data1/cache/VEP/` * Path to `vep_cache`: `/data1/cache/VEP/`
* Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz` * Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
* Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi` * Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi`
* Load module `Sentieon` for Process with `sentieon` labels * Load module `Sentieon` for Processes with `sentieon` labels

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pipeline/sarek.config
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@ -10,4 +10,4 @@
profiles { profiles {
munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" } munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
} }