diff --git a/docs/ngs-dependencies.md b/docs/ngs-dependencies.md index af0f86f6..8c025ddb 100644 --- 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 index eadfea33..5acbdcec 100644 --- 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 index be3f006b..f0f27d85 100644 --- 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 index ec0fdd96..5bcd13bc 100644 --- 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 index 688e568a..c92cc5b1 100755 --- 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 index 9e758978..e3aabb93 100644 --- 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