From 9fb5715c4ca0ef33c0227ddab697b0f0d0c4e575 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Tue, 5 Mar 2019 16:12:39 +0100
Subject: [PATCH] Added support for new params.custom_config_base option

---
 README.md            | 27 +++++++++++++++++++++++++--
 nfcore_custom.config |  2 +-
 2 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 6d5b340..593e61b 100644
--- a/README.md
+++ b/README.md
@@ -16,7 +16,7 @@ A repository for hosting nextflow config files containing custom parameters requ
 
 ## Using an existing config
 
-The Nextflow [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter can be used with nf-core pipelines in order to load custom config files that you have available locally. However, if you or other people within your organisation are likely to be running nf-core pipelines regularly it may be a good idea to use/create a custom config file that defines some generic settings unique to the computing environment within your organisation. 
+The Nextflow [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter can be used with nf-core pipelines in order to load custom config files that you have available locally. However, if you or other people within your organisation are likely to be running nf-core pipelines regularly it may be a good idea to use/create a custom config file that defines some generic settings unique to the computing environment within your organisation.
 
 ### Configuration and parameters
 
@@ -28,7 +28,30 @@ You should be able to get a good idea as to how other people are customising the
 
 ### Offline usage
 
-If you want to use an existing config available in `nf-core/configs`, and you're running on a system that has no internet connection, you'll need to download the config file and place it in a location that is visible to the file system on which you are running the pipeline. You can then run the pipeline with the `-c` parameter - see [Testing](#testing) for example.
+If you want to use an existing config available in `nf-core/configs`, and you're running on a system that has no internet connection, you'll need to download the config file and place it in a location that is visible to the file system on which you are running the pipeline. Then run the pipeline with `--custom_config_base`
+or `params.custom_config_base` set to the location of the directory containing the repository files:
+
+```bash
+## Download and unizp the config files
+cd /path/to/my/configs
+wget https://github.com/nf-core/configs/archive/master.zip
+unzip master.zip
+
+## Run the pipeline
+cd /path/to/my/data
+nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
+```
+
+Alternatively, instead of using the configuration profiles from this repository, you can run your
+pipeline directly calling the single institutional config file that you need with the `-c` parameter.
+
+```bash
+## Example command for nf-core/rnaseq
+nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_config.config ..
+```
+
+> Note that the nf-core/tools helper package has a `download` subcommand download required
+> pipeline files for you to make this process easier.
 
 ## Adding a new config
 
diff --git a/nfcore_custom.config b/nfcore_custom.config
index 757b70b..2e4139c 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -8,7 +8,7 @@
  * name here.
  */
 
-config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/conf"
+config_base = "${params.custom_config_base}/conf"
 
 profiles {
   binac        { includeConfig "${config_base}/binac.config" }