Feature request: Integrate QC Tools like FASTQC and Qualimap

[berntpopp]

Feature request: Integrate QC Tools like FASTQC and Qualimap

Description:
Integrate quality control tools like FASTQC and Qualimap into the workflow to ensure data quality at various stages of the pipeline.

Acceptance Criteria:

• Integrate FASTQC and Qualimap into the relevant steps of the workflow.
• Ensure QC reports are generated for each relevant stage.
• Update the documentation to include the usage of QC tools.

Implementation Steps:

1. Integrate FASTQC into the workflow to check the quality of input FASTQ files.
2. Integrate Qualimap to assess the quality of BAM files.
3. Ensure QC reports are generated and saved in the designated directory.
4. Test the workflow with sample data to ensure QC tools are working as expected.
5. Update the documentation with instructions on interpreting QC reports.