Commit 33fad7e1 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Fix some explaination about the output directories in the config

parent e67d71a0
......@@ -136,8 +136,23 @@ Setting up the pipeline is done within the pipeline itself, fine-tuning is alway
### Config setup
For our new pipeline, one should setup the (default) config options.
Since our pipeline is called `HelloPipeline`, the root of the configoptions will called `hellopipeline` (lowercaps).
```json
{
"output_dir": "/home/user/mypipelineoutpt",
"hellopipeline": {
}
}
```
### Test pipeline
### Summary output
### Reporting output (opt)
\ No newline at end of file
### Reporting output (optional)
\ No newline at end of file
......@@ -8,12 +8,14 @@ The sample config should be in [__JSON__](http://www.json.org/) or [__YAML__](ht
- Second field should contain the __"libraries"__
- Third field contains __"R1" or "R2"__ or __"bam"__
- The fastq input files can be provided zipped and unzipped
- `output_dir` is a required setting that should be set either in a `config.json` or specified on the invocation command via -cv output_dir=<path/to/outputdir\>. The default value is to place the pipeline output in the current working directory.
#### Example sample config
###### yaml:
``` yaml
output_dir: /home/user/myoutputdir
samples:
Sample_ID1:
libraries:
......@@ -26,6 +28,7 @@ samples:
``` json
{
"output_dir": "/home/user/myoutputdir",
"samples":{
"Sample_ID1":{
"libraries":{
......
......@@ -52,7 +52,7 @@ Specific configuration options additional to Basty are:
```json
{
output_dir: </path/to/out_directory>,
"output_dir": </path/to/out_directory>,
"shiva": {
"variantcallers": ["freeBayes"]
},
......
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