@@ -70,9 +70,9 @@ In the `tags` key inside a sample or library users can supply tags that belong t
The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
This config file should be written in either JSON or YAML format. It can contain setup settings like:
* references,
* cut offs,
* program modes and memory limits (program specific),
* references
* cut offs
* program modes and memory limits (program specific)
* Whether chunking should be used
* set program executables (if for some reason the user does not want to use the systems default tools)
* One could set global variables containing settings for all tools used in the pipeline or set tool specific options one layer
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@@ -128,9 +128,13 @@ It is also possible to set the `"species"` flag. Again, we will default to `unkn
# More advanced use of config files.
### 4 levels of configuring settings
In biopet, a value of a ConfigNamespace (e.g., "reference_fasta") for a tool or a pipeline can be defined in 4 different levels.
* Level-4: As a fixed value hardcoded in biopet source code
* Level-3: As a user specified value in the user config file
* Level-2: As a system specified value in the global config files. On the LUMC's SHARK cluster, these global config files are located at /usr/local/sasc/config.
* Level-1: As a default value provided in biopet source code.
During execution, biopet framework will resolve the value for each ConfigNamespace following the order from level-4 to level-1. Hence, a value defined in the a higher level will overwrite a value define in a lower level for the same ConfigNamespace.
| -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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| | --expert | | This flag enables the user to configure a more extensive list of parameters for the pipeline. |
This pipeline is build for variant calling on NGS data (preferably Illumina data).
It is based on the <ahref="https://www.broadinstitute.org/gatk/guide/best-practices"target="_blank">best practices</a>) of GATK in terms of their approach to variant calling.
This pipeline is built for variant calling on NGS data (preferably Illumina data). Part of this pipeline resembles the <ahref="https://www.broadinstitute.org/gatk/guide/best-practices"target="_blank">best practices</a>) of GATK in terms of their approach to variant calling.
The pipeline accepts ```.fastq & .bam``` files as input.
----
## Tools for this pipeline
## Overview of tools and sub-pipelines for this pipeline
Note that one should first create the appropriate [configs](../general/config.md).
Note that one should first create the appropriate sample and pipeline setting [configs](../general/config.md).
### Sample input extensions
Shiva pipeline can start from FASTQ or BAM files. This pipeline will include pre-process steps for the BAM files.
Please refer [to our mapping pipeline](mapping.md) for information about how the input samples should be handled.
Shiva is a special pipeline in the sense that it can also start directly from `bam` files. Note that one should alter the sample config field from `R1` into `bam`.
### Full pipeline
The full pipeline can start from fastq or from bam file. This pipeline will include pre-process steps for the bam files.
When using BAM files as input, Note that one should alter the sample config field from `R1` into `bam`.
A dry run can be performed by simply removing the `-run` flag from the command line call.
[Gears](gears) is run automatically for the data analysed with `Shiva`. There are two levels on which this can be done and this should be specified in the [config](../general/config) file:
*`mapping_to_gears: unmapped` : Unmapped reads after alignment. (default)
*`mapping_to_gears: all` : Trimmed and clipped reads from [Flexiprep](flexiprep).
*`mapping_to_gears: none` : Disable this functionality.
