From 283abcece42074eead291e67166dbdc0b2d3ffba Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 20 Nov 2019 15:32:35 +0100 Subject: [PATCH] update docs --- README.md | 6 +++++- docs/pipeline/sarek/munin.md | 7 ++++--- pipeline/sarek.config | 2 +- 3 files changed, 10 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 9e40d67..06bd456 100644 --- a/README.md +++ b/README.md @@ -12,6 +12,10 @@ A repository for hosting nextflow config files containing custom parameters requ * [Testing](#testing) * [Documentation](#documentation) * [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) ## Using an existing config @@ -128,7 +132,7 @@ Currently documentation is available for the following pipelines within the spec * sarek * [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/` repository. diff --git a/docs/pipeline/sarek/munin.md b/docs/pipeline/sarek/munin.md index 24c4404..cd93648 100644 --- a/docs/pipeline/sarek/munin.md +++ b/docs/pipeline/sarek/munin.md @@ -10,12 +10,13 @@ This will download and launch the [`munin.config`](../conf/pipeline/sarek/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 `vep_cache`: `/data1/cache/VEP/` * Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz` * Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi` -* Load module `Sentieon` for Process with `sentieon` labels \ No newline at end of file +* Load module `Sentieon` for Processes with `sentieon` labels \ No newline at end of file diff --git a/pipeline/sarek.config b/pipeline/sarek.config index aed6a1d..9457972 100644 --- a/pipeline/sarek.config +++ b/pipeline/sarek.config @@ -10,4 +10,4 @@ profiles { munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" } -} +} \ No newline at end of file