Bumped version, updated docs.

Author: ewels

CHANGELOG.md

@@ -1,10 +1,11 @@
 # NGI-MethylSeq
 
-## v0.3dev
+## [v0.3](https://github.com/SciLifeLab/NGI-MethylSeq/releases/tag/0.3) - 2017-09-01
 * Fix `--rrbs` mode ([#24](https://github.com/SciLifeLab/NGI-MethylSeq/issues/24))
 * Fixed fairly major bug where only a single sample would run past alignment
 * Merged test scripts and rewrote to use command line flags / new travis script.
 * Refactored software version collection code to be more resilient and cleaner / easier to maintain.
+* Dropped support for environment modules and added support for use of Singularity on UPPMAX
 
 ## [v0.2](https://github.com/SciLifeLab/NGI-MethylSeq/releases/tag/0.2) - 2017-07-17
 First (semi-) stable release of the new NGI-MethylSeq pipeline, as we head towards deployment in production.

docs/installation.md

@@ -142,16 +142,20 @@ If you are able to use [Docker](https://www.docker.com/), you can use the [sclif
 
 We recommend using [Bioconda](https://bioconda.github.io/) to install the required software as the process is quite easy in our experience.
 
-## 3.3) Configuration: Docker
+## 3.3) Configuration: Docker and Singularity
 Docker is a great way to run NGI-MethylSeq, as it manages all software installations and allows the pipeline to be run in an identical software environment across a range of systems.
 
-Nextflow has [excellent integration](https://www.nextflow.io/docs/latest/docker.html) with Docker, and beyond installing the two tools, not much else is required.
+On UPPMAX, we use this pipeline with [Singularity](http://singularity.lbl.gov/) instead of Docker. Singularity similar to Docker, but designed for long-running jobs in HPC environments.
+Singularity images are automatically created from Docker images, so only a Docker image has to be maintained.
 
+Nextflow has [excellent integration](https://www.nextflow.io/docs/latest/docker.html) with Docker and Singularity, and beyond installing Nextflow and Docker / Singularity, not much else is required.
+
+#### Docker
 First, install docker on your system : [Docker Installation Instructions](https://docs.docker.com/engine/installation/)
 
 Then, simply run the analysis pipeline:
 ```bash
-nextflow run SciLifeLab/NGI-MethylSeq -profile docker # rest of normal launch command
+nextflow run SciLifeLab/NGI-MethylSeq -profile base -with-docker scilifelab/ngi-methylseq # rest of normal launch command
 ```
 
 Nextflow will recognise `SciLifeLab/NGI-MethylSeq` and download the pipeline from GitHub. The `-profile docker` configuration lists the [sclifelab/ngi-methylseq](https://hub.docker.com/r/scilifelab/ngi-methylseq/) image that we have created and is hosted at dockerhub, and this is downloaded.
@@ -160,6 +164,15 @@ A reference genome is still required by the pipeline. Specifying a path to a FAS
 
 A test suite for docker comes with the pipeline, and can be run by moving to the [`tests` directory](https://github.com/ewels/NGI-MethylSeq/tree/master/tests) and running `./docker_test.sh`. This will download a small lambda genome and some data, and attempt to run the pipeline through docker on that small dataset. This is automatically run using [Travis](https://travis-ci.org/SciLifeLab/NGI-MethylSeq/) whenever changes are made to the pipeline.
 
+#### Singularity
+Running with singularity is very similar. Nextflow will pull the docker image from dockerhub, build a singularity image from this and run using that.
+
+The command is as follows:
+```bash
+nextflow run SciLifeLab/NGI-MethylSeq -profile base -with-singularity docker://scilifelab/ngi-methylseq # rest of normal launch command
+```
+
+
 ## 3.4) Configuration: Amazon EC2
 There are multiple ways of running this pipeline over Amazon's EC2 service. Please see the [NGI-RNAseq pipeline docs](https://github.com/SciLifeLab/NGI-RNAseq/blob/master/docs/amazon_web_services.md) for more information.
 

docs/usage.md

@@ -186,12 +186,7 @@ projects or different sets of reference genomes.
 
 **NB:** Single hyphen (core Nextflow option)
 
-Note - you can use this to override defaults. For example, we run on UPPMAX but don't want to use the MultiQC
-environment module as is the default. So we specify a config file using `-c` that contains the following:
-
-```groovy
-process.$multiqc.module = []
-```
+Note - you can use this to override defaults.
 
 ### `--clusterOptions`
 Submit arbitrary SLURM options (UPPMAX profile only). For instance, you could use `--clusterOptions '-p devcore'`

nextflow.config

@@ -34,6 +34,9 @@ profiles {
   testing {
     includeConfig 'conf/testing.config'
   }
+  base {
+    includeConfig 'conf/base.config'
+  }
   none {
     // Don't load any config (for use with custom home configs)
   }