From 47ad6f45bf0a70322519fd1995701ac3dfc367fa Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Sat, 15 Dec 2018 22:44:57 +0100 Subject: [PATCH] Document me :-) --- docs/configuration/reference_genomes.md | 1 - docs/usage.md | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/configuration/reference_genomes.md b/docs/configuration/reference_genomes.md index b0ac327a8..324cfef07 100644 --- a/docs/configuration/reference_genomes.md +++ b/docs/configuration/reference_genomes.md @@ -10,7 +10,6 @@ Read [Adding your own system](adding_your_own.md) to find out how to set up cust ## Adding paths to a config file Specifying long paths every time you run the pipeline is a pain. To make this easier, the pipeline comes configured to understand reference genome keywords which correspond to preconfigured paths, meaning that you can just specify `--genome ID` when running the pipeline. ->>>>>>> TEMPLATE Note that this genome key can also be specified in a config file if you always use the same genome. diff --git a/docs/usage.md b/docs/usage.md index 8a90a3a25..053406816 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -136,7 +136,7 @@ If you prefer, you can specify the full path to your reference genome when you r ```bash --fasta '[path to Fasta reference]' ``` -> If you don't specify appropriate `--bwa_index`, `--fasta_index` parameters, the pipeline will create these indices for you automatically. Note, that saving these for later has to be turned on using `--saveReference`. +> If you don't specify appropriate `--bwa_index`, `--fasta_index` parameters, the pipeline will create these indices for you automatically. Note, that saving these for later has to be turned on using `--saveReference`. You may also specify the path to a gzipped (`*.gz` file extension) FastA as reference genome - this will be uncompressed by the pipeline automatically for you. ### `--genome` (using iGenomes)