Metadata-Version: 2.1
Name: bonsai-prp
Version: 0.5.0
Summary: Pipline result processing program for the JASEN pipeline and Bonsai tool.
Author-email: Markus Johansson <markus.h.johansson@skane.se>, Ryan Kennedy <Ryan.Kennedy@skane.se>
Project-URL: Repository, https://github.com/Clinical-Genomics-Lund/
Project-URL: Issues, https://github.com/Clinical-Genomics-Lund/bonsai-prp/issues
Project-URL: Changelog, https://github.com/Clinical-Genomics-Lund/CHANGELOG.md
Classifier: Development Status :: 3 - Alpha
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: setuptools
Requires-Dist: wheel
Requires-Dist: click ==8.1.7
Requires-Dist: pydantic ==2.5.2
Requires-Dist: pandas ==2.1.3
Requires-Dist: pysam
Provides-Extra: dev
Requires-Dist: pylint ~=3.0.2 ; extra == 'dev'
Requires-Dist: black ~=23.11.0 ; extra == 'dev'
Requires-Dist: isort ~=5.12.0 ; extra == 'dev'
Provides-Extra: test
Requires-Dist: pytest-cov ~=4.1.0 ; extra == 'test'

# Pipeline result processor (prp): A collection of parsers and data models for creation and validation of a standardized output for the [jasen](https://github.com/genomic-medicine-sweden/jasen) pipeline which is used as an input for [bonsai](https://github.com/Clinical-Genomics-Lund/bonsai)

## Dependencies (latest)
* biopython
* pydantic=2.5.3
* python=3.10

## Using prp
### Use the help argument for information regarding the prp's methods
```
prp --help
```

### Use the method help argument for information regarding the input for each of prp's methods (`create-bonsai-input`, `create-cdm-input`, `create-qc-result`, `print-schema`, `validate`)
```
prp <method> --help
```

### Create bonsai input from pipeline data
```
prp create-bonsai-input -i SAMPLE_ID -u RUN_METADATA_FILE -q QUAST_FILENAME -d PROCESS_METADATA_FILE -k KRAKEN_FILE -a AMRFINDER_FILE -m MLST_FILE -c CGMLST_FILE -v VIRULENCEFINDER_FILE -r RESFINDER_FILE -p POSTALIGNQC_FILE -k MYKROBE_FILE -t TBPROFILER_FILE [--correct_alleles] -o OUTPUT_FILE [-h]
```

### Create CDM input from pipeline data
```
prp create-cdm-input -q QUAST_FILENAME -c CGMLST_FILE -p POSTALIGNQC_FILE [--correct_alleles] -o OUTPUT_FILE [-h]
```

### Create QC result from bam file
```
prp create-qc-result -i SAMPLE_ID --b BAM_FILE [-e BED_FILE] [-a BAITS_FILE] -r REFERENCE_FILE [-c CPUS] -o OUTPUT_FILE [-h]
```
