Pipelines¶
Bam QC Tool¶
This is a pipeline using BamQC for bam file stats.
Running from the command line¶
Parameters¶
- config : file
- Location of the config file for the workflow
- in_metadata : file
- Location of the input list of files required by the process
- out_metadata : file
- Location of the output results.json file for returned files
Returns¶
- output : file
- Html file with all the statistics
Example¶
When using a local verion of the [COMPS virtual machine](http://www.bsc.es/computer-sciences/grid-computing/comp-superscalar/downloads-and-documentation):
1 2 | cd /home/compss/code/Bam_QC
runcompss --lang=python Bam_QC/process_bamqc.py --config /home/compss/code/Bam_QC/tool_config/process_bamqc.json --in_metadata /home/compss/code/Bam_QC/tests/json/input_bamqc.json --out_metadata /home/compss/code/Bam_QC/tests/results.json
|
Methods¶
-
class
process_bamqc.
process_bamqc
(configuration=None)[source]¶ Functions for demonstrating the pipeline set up.
-
run
(input_files, metadata, output_files)[source]¶ This pipeline analyses a given bam file and produces html file as the reporting output file.
Parameters: - input_files (dict) –
Dictionary of file locations. These should include:
- bam : str
- Location for the bam file
- metadata (list) – Required meta data
- output_files (dict) – Locations of the output html files returned by the pipeline
Returns: - output_files (dict) – Locations for the output html
- output_metadata (dict) – Matching metadata for each of the files
- input_files (dict) –
-