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):

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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