Commit ea8b1d5c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge remote-tracking branch 'remotes/origin/develop' into release-0.8.0

# Conflicts:
#	docs/general/
parents 3ec7db11 d92b2c9c
......@@ -17,10 +17,14 @@ node('local') {
stage('Report tests') {
stage('Report Tests') {
junit '*/target/surefire-reports/*.xml'
stage('Check Documentation') {
sh 'mkdocs build --clean --strict'
if(currentBuild.result == null || "SUCCESS".equals(currentBuild.result)) {
currentBuild.result = "SUCCESS"
slackSend (color: '#00FF00', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
......@@ -60,7 +60,7 @@ samples:
bam: MySecond.bam
Note that there is a tool called [SamplesTsvToJson](../tools/ this enables a user to get the sample config without any chance of creating a wrongly formatted JSON file.
Note that there is a tool called [SamplesTsvToConfig](../tools/ that enables the user to get the sample config without any chance of creating a wrongly formatted file.
#### Tags
......@@ -139,3 +139,37 @@ During execution, biopet framework will resolve the value for each ConfigNamespa
To check if the created JSON file is correct their are several possibilities: the simplest way is using [this](
website. It is also possible to use Python, Scala or any other programming languages for validating JSON files but this requires some more knowledge.
#Creating config files with Biopet
With the pipelines Gentrap, MultiSampleMapping and Shiva it is possible to use Biopet itself for creating the config files. Biopet should be called with the keyword *template* and the user will be then prompted to enter the values for the parameters needed by the pipelines. Biopet will generate a config file that can be used as input when running the pipelines. The purpose is to ease the step of creating the config files. It is useful especially when Biopet has been pre-configured to use a list of reference genomes. Then the user needs only to specify which refence genome he/she wants to use and the location of the reference genome files can be derived from Biopet's global configuration.
<b> Example </b>
For viewing the pipelines for which this functionality is supported:
``` bash
biopet template
For getting help about using it for a specific pipeline:
``` bash
biopet template Gentrap -h
For running the tool:
``` bash
biopet template Gentrap -o gentrap_config.yml -s
<b> Description of the parameters </b>
| Flag (short)| Flag (long) | Type | Function |
| ------------ | ----------- | ---- | -------- |
| -o | --outputConfig | Path (**required**) | Name of the config file that gets generated.|
| -s | --outputScript | Path (optional) | Biopet can also output a script that can be directly used for running the pipeline, the call of the pipeline is generated with the config file as input. This parameter sets the name for the script file.|
| -t | --template | Path (optional) | A template file with 2 placeholders *%s* is required for generating the script. The first placeholder will be replaced with the name of the pipeline, the second with the paths to the sample and settings config files. When Biopet has been pre-configured to use the default template file, then setting this parameter is optional. |
| | --expert | | This flag enables the user to configure a more extensive list of parameters for the pipeline. |
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