Merge pull request #232 from RoanKanninga/master

updated docs + updated version in generate_template
molgenis · Dec 19, 2018 · e318240 · e318240
2 parents a4af5db + 30597f1
commit e318240
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Showing 6 changed files with 13 additions and 9 deletions.
diff --git a/docs/ngs-dependencies.md b/docs/ngs-dependencies.md
@@ -1,4 +1,4 @@
-### NGS_DNA-3.5.1 pipeline dependencies
+### NGS_DNA-3.5.2 pipeline dependencies
 ```
 ('BWA', '0.7.15', '', ('foss', '2015b')),
 ('BEDTools', '2.25.0', '', ('foss', '2015b')),

diff --git a/docs/ngs-install.md b/docs/ngs-install.md
@@ -9,7 +9,7 @@ The NGS_DNA pipeline has a lot of dependencies, these are handled by easybuild w
 
 **_Note:_** the order in which you give the paths are important! To original easybuild path can be left empty (just a colon is enough)
 ```bash
-eb NGS_Automated/2.0.13-NGS_DNA-3.5.1.eb --robot --robot-paths=${pathToMYeasybuild}/easybuild-easyconfigs/easybuild/easyconfigs/:
+eb NGS_Automated/2.0.13-NGS_DNA-3.5.2.eb --robot --robot-paths=${pathToMYeasybuild}/easybuild-easyconfigs/easybuild/easyconfigs/:
 ```
 **_Note:_** some software cannot be downloaded automagically due to for example licensing or technical issues and the build will fail initially.
 In these cases you will have to download manually and copy the sources to

diff --git a/docs/ngs-latestrelease.md b/docs/ngs-latestrelease.md
@@ -2,12 +2,16 @@
 
 ## Is in use since 05-12-2018 (December 5th 2018)
 
-download here: https://github.com/molgenis/NGS_DNA/releases/tag/3.5.1
+download here: https://github.com/molgenis/NGS_DNA/releases/tag/3.5.2
 
-## Release notes 3.5.1:
-
-** updated docs **
+## Release notes 3.5.2 (and 3.5.1):
+### 3.5.2
+- added GavinStandAlone to the NGS_DNA repo
+- updated docs
+- tiny bugs in the dependencies in the workflow
+- bugfix in GenderCalculate, when there is noChrX it will produces an error due to missing initialisation of a variable
 
+### 3.5.1
 ** updated **
 - changed prm/cluster for diagnostics 
 - decreased resources used in some protocols

diff --git a/docs/ngs-quickstart.md b/docs/ngs-quickstart.md
@@ -5,7 +5,7 @@ This is the Quick tutorial, when there are problems first go to the detailed [in
 We first have to load EasyBuild, this can be done with this command
 ```bash
 module load EasyBuild
-eb NGS_DNA-3.5.1.eb --robot -–robot-paths=${pathToMYeasybuild}/easybuild-easyconfigs/easybuild/easyconfigs/:
+eb NGS_DNA-3.5.2.eb --robot -–robot-paths=${pathToMYeasybuild}/easybuild-easyconfigs/easybuild/easyconfigs/:
 ```
 **_Note:_** some software cannot be downloaded automagically due to for example licensing or technical issues and the build will fail initially.
 In these cases you will have to download manually and copy the sources to

diff --git a/templates/generate_template.sh b/templates/generate_template.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-module load NGS_DNA/3.5.1
+module load NGS_DNA/3.5.2
 module list
 host=$(hostname -s)
 environmentParameters="parameters_${host}"

diff --git a/test/test_pipeline.sh b/test/test_pipeline.sh
@@ -147,7 +147,7 @@ cd "${pipelinefolder}"
 echo "pr number: $1"
 
 PULLREQUEST="${1}"
-NGS_DNA_VERSION=NGS_DNA/3.5.1
+NGS_DNA_VERSION=NGS_DNA/3.5.2
 
 git clone https://github.com/molgenis/NGS_DNA.git
 cd NGS_DNA