Bump pipeline version to v1.4

SciLifeLab · Mar 26, 2018 · 077287d · 077287d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # NGI-RNAseq
 
-## 1.4dev
+## [1.4](https://github.com/SciLifeLab/NGI-RNAseq/releases/tag/1.4) - 2018-03-26
 The version 1.4 release contains major improvements to the NGI-RNAseq pipeline, especially focussed on the portability of the pipeline. Hopefully these changes will make it significantly easier for people to use the pipeline in different compute environments.
 
 Many thanks to everyone who gave us feedback about the pipeline!

diff --git a/conf/uppmax-modules.config b/conf/uppmax-modules.config
@@ -41,7 +41,7 @@ process {
     'bioinfo-tools',
     'FastQC/0.11.5',
     'HISAT2/2.1.0',
-    'MultiQC/1.3',
+    'MultiQC/1.4',
     'picard/2.10.3',
     'preseq/0.1.0',
     'rseqc/2.6.1',

diff --git a/docs/configuration/adding_your_own.md b/docs/configuration/adding_your_own.md
@@ -51,7 +51,7 @@ nextflow run SciLifeLab/NGI-RNAseq -profile docker --reads '<path to your reads>
 
 Nextflow will recognise `SciLifeLab/NGI-RNAseq` and download the pipeline from GitHub. The `-profile docker` configuration lists the [sclifelab/ngi-rnaseq](https://hub.docker.com/r/scilifelab/ngi-rnaseq/) image that we have created and is hosted at dockerhub, and this is downloaded.
 
-The public docker images are tagged with the same version numbers as the code, which you can use to ensure reproducibility. When running the pipeline, specify the pipeline version with `-r`, for example `-r v1.3`. This uses pipeline code and docker image from this tagged version.
+The public docker images are tagged with the same version numbers as the code, which you can use to ensure reproducibility. When running the pipeline, specify the pipeline version with `-r`, for example `-r v1.4`. This uses pipeline code and docker image from this tagged version.
 
 To add docker support to your own config file (instead of using the `docker` profile, which runs locally), add the following:
 

diff --git a/docs/configuration/local.md b/docs/configuration/local.md
@@ -19,7 +19,7 @@ Nextflow will recognise `SciLifeLab/NGI-RNAseq` and download the pipeline from G
 For more information about how to work with reference genomes, see [`docs/configuration/reference_genomes.md`](docs/configuration/reference_genomes.md).
 
 ### Pipeline versions
-The public docker images are tagged with the same version numbers as the code, which you can use to ensure reproducibility. When running the pipeline, specify the pipeline version with `-r`, for example `-r v1.3`. This uses pipeline code and docker image from this tagged version.
+The public docker images are tagged with the same version numbers as the code, which you can use to ensure reproducibility. When running the pipeline, specify the pipeline version with `-r`, for example `-r v1.4`. This uses pipeline code and docker image from this tagged version.
 
 
 ## Singularity image

diff --git a/docs/configuration/uppmax.md b/docs/configuration/uppmax.md
@@ -35,8 +35,8 @@ or `.tar.gz` file). Once transferred, extract the pipeline files.
 For example, with a `.zip` file:
 
 ```bash
-unzip 1.3.1.zip
-mv NGI-RNAseq-1.3.1 NGI-RNAseq # rename the folder
+unzip 1.4.zip
+mv NGI-RNAseq-1.4 NGI-RNAseq # rename the folder
 cd NGI-RNAseq
 pwd # Prints full path to your pipeline
 ```
@@ -51,6 +51,10 @@ nextflow run /path/to/NGI-RNAseq -with-singularity /path/to/singularity/ngi-rnas
 
 (Note that you'll need the other common flags such as `--reads` and `--genome` in addition to this command).
 
+> NB: Note that you should _not_ use the `-r 1.4` flag recommended elsewhere. This tells Nextflow to download
+> that version of the code when it runs. Here, you have already downloaded the code, so it generates an error.
+
+
 ## Environment modules and development
 If you would prefer to use environment modules instead of singularity, you can use the old version of the configuration by specifying `-profile uppmax_modules` (we don't recommend this).
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -36,7 +36,7 @@ nextflow pull scilifelab/ngi-rnaseq
 ### Reproducibility
 It's a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
-First, go to the [NGI-RNAseq releases page](https://github.com/SciLifeLab/NGI-RNAseq/releases) and find the latest version number - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`.
+First, go to the [NGI-RNAseq releases page](https://github.com/SciLifeLab/NGI-RNAseq/releases) and find the latest version number - numeric only (eg. `1.4`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.4`.
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
 

diff --git a/nextflow.config b/nextflow.config
@@ -15,8 +15,8 @@ params {
   outdir = './results'
   igenomes_base = 's3://ngi-igenomes/igenomes/'
   clusterOptions = false
-  
-  version = '1.4dev' //Pipeline version
+
+  version = '1.4' //Pipeline version
   nf_required_version = '0.27.6' //Minimum version of Nextflow required
   container = 'scilifelab/ngi-rnaseq' // Container slug. Stable releases should specify release tag!
 }