Merge pull request #3 from ewels/master

Started results docs.

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).
 
-<p align="center"><a href="stand_alone/http://www.scilifelab.se/" target="_blank"><img src="Docs/images/SciLifeLab_logo.png" title="SciLifeLab"></a></p>
+<p align="center"><a href="stand_alone/http://www.scilifelab.se/" target="_blank"><img src="docs/images/SciLifeLab_logo.png" title="SciLifeLab"></a></p>

docs/README.md

@@ -0,0 +1,3 @@
+# NGI-MethylSeq Results
+
+This document is not yet written sorry, come back soon!