Pipline result processing program for the JASEN pipeline and Bonsai tool.
Project description
Pipeline result processor (prp)
A collection of parsers and data models for creation and validation of a standardized output for the jasen pipeline which is used as an input for bonsai.
[!WARNING] Bonsai-PRP is under development in an alpha stage. Expect uneven documentation, breaking changes, and bugs until the official 1.0 release.
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 (add-igv-annotation-track
, annotate-delly
, create-bonsai-input
, create-cdm-input
, create-qc-result
, print-schema
, rerun-bonsai-input
, 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 --vcf VCF_FILE [--snv-vcf SNV_VCF_FILE] [--sv-vcf SV_VCF_FILE] [--symlink-dir SYMLINK_DIR] [--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]
Rerun bonsai input creation for all samples
prp rerun-bonsai-input -i INPUT_DIR -j JASEN_DIR -s SYMLINK_DIR -o OUTPUT_DIR -o OUTPUT_FILE [-h]
Add IGV annotation track to result
prp add-igv-annotation-track -n TRACK_NAME -a ANNOTATION_FILE -b BONSAI_INPUT_FILE -o OUTPUT_FILE [-h]
Validate output format of result json file
prp validate -o OUTPUT_FILE [-h]
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