diff --git a/README.md b/README.md
index 153c6e2..1067e0e 100644
--- a/README.md
+++ b/README.md
@@ -8,6 +8,10 @@ This pipeline is currently under active development and has very little in the w
There's a pretty good chance that it won't run. Any help debugging is very welcome! Please
fork, make changes and submit a pull request.
+## Pipeline Results
+See the [pipeline documentation](docs/README.md) for explanations of
+the results files.
+
## Installation
### NextFlow installation
To use this pipeline, you need to have a working version of NextFlow installed. You can find more
@@ -18,11 +22,19 @@ of NextFlow looks like this:
curl -fsSL get.nextflow.io | bash
mv ./nextflow ~/bin
```
-Note that if you're running on a Swedish UPPMAX cluster you can load NextFlow as an environment module:
+
+#### UPPMAX
+If you're running on a Swedish UPPMAX cluster you can load NextFlow as an environment module instead:
```
module load nextflow
```
+The first time you load this you will get a warning about setting environment variables. To automatically set these at login, you can add the following lines to your `~/.bashrc` file:
+```bash
+export NXF_LAUNCHBASE=$SNIC_TMP
+export NXF_TEMP=$SNIC_TMP
+```
+
### NextFlow configuration
Next, you need to set up a config file so that NextFlow knows how to run and where to find reference
indexes. You can find an example configuration file for UPPMAX (milou) with this repository:
@@ -111,4 +123,4 @@ These scripts were written for use at the [National Genomics Infrastructure](htt
at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden.
Written by Phil Ewels (@ewels) and Rickard Hammarén (@Hammarn).
-
+
diff --git a/docs/README.md b/docs/README.md
new file mode 100644
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--- /dev/null
+++ b/docs/README.md
@@ -0,0 +1,3 @@
+# NGI-MethylSeq Results
+
+This document is not yet written sorry, come back soon!
\ No newline at end of file
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