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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]