v3.0.1 - update to v10.0-1 HIVDB comment reference file paths

An automated version update to Stanford HIVDB to v10.0-1 required updating the comment reference files used for report generation. These reference file versions are now also logged in the decipher_tool_versions_*.csv file.

v3.0.0 - Major Updates

Github release v3.0.0
Updates to bcl2deciPHEr_runner.sh:

• Updated sbatch commands to limit job submissions to a single host and slurm log names to reflect job name.
• Updated to execute HIV_sierrapy reporting script.
• Updates to the config.yaml file generation to read the samplesheet and designate the requested virus (this now controls which virus specific part of the pipeline is run).

Updates to Snakefile_deciPHEr_QC:

• Implemented a QC_checkpoint_summary.tsv file that merges all QC outputs checked for pipeline progression to occur.
• Updated the generation of the QC_checkpoint_config.yaml to check the original config.yaml for the requested virus and for QC metrics to decide pathway for downstream processing.

Updates to Snakefile_deciPHEr_HIV2, Snakefile_deciPHEr_HCV2, and Snakefile_deciPHEr_HBV2:

• Updated all rules to run only if the HIV/HCV/HBV is specified in the QC_checkpoint_config.yaml (prevents failed snakemake execution for these parts of the pipeline).
• Implemented a HIV/HCV/HBV_QC_summary.tsv file that merges all QC outputs checked for virus-specific QC to be performed.
• Implemented a QC_HIV_reporting_config.yaml file to check for HIV samples that pass QC metrics for polymerase drug resistance analysis and reporting.

Implemented automated report generation of HIV drug resistance analysis via the Stanford HIVDB command-line tool sierrapy:

• Implemented a HIV_sierrapy_runner.sh script to check for a QC_HIV_reporting_config.yaml file, and if it exists execute the Snakefile_HIV_sierrapy file.
• Implemented a Snakefile_HIV_sierrapy file that executes sierrapy command-line submission to the back-end of the Stanford HIVDB website for raw data collection,
  then executes the decipher_sierrapy_reporting.py script that generates the final drug resistance report in an excel format (only performed on HIV that pass QC metrics for polymerase drug resistance analysis and reporting).
• Implemented a decipher_sierrapy_reporting.py script that takes raw data from sierrapy and converts this into a final drug resistance report in an excel format.

Updates to decipher_tool_version_record.sh:

• Updated pipeline version printed to output.
• Updated to include seirrapy and decipher_sierrapy_reporting.py versions printed to output.

v2.0.1

Added a QC summary sheet for negative control data.

v2.0.0

Consolidated conda environments used for each tool, updated base-calling script to produce a log file of all the tool versions, updated the annotated bammix files for easier reading.

v1.0.0

The decipher pipeline is now automated for HBV, HCV and HIV analysis. This includes an auto-run step for the output of each read-mapping tool when contig correction is not required.