README.md

Jasentool: A mongodb validation tool for comparing pipeline outputs

Dependencies (latest)

• python=3.11
• pymongo

Using Jasentool

Use the help argument for information regarding the Jasentool's methods

jasentool -h

Use the method help argument for information regarding the input for each of Jasentool's methods (find, insert, remove, validate, missing, fix, convert, converge, qc)

jasentool <method> -h

Validate pipeline data

jasentool validate (-i INPUT_FILE [INPUT_FILE ...] | --input_dir INPUT_DIR) --db_name DB_NAME --db_collection DB_COLLECTION -o OUTPUT_FILE [--address ADDRESS] [-h]

Find missing samples

jasentool missing --db_name <db_name> --db_collection <db_collection> --analysis_dir <jasen_analysis_results_dir> --restore_dir <restore_dir> --restore_file <restore_file.sh> -o <output_file.csv>

Fix bjorn csv

jasentool fix --csv_file /data/tmp/multi_microbiology.csv --sh_file /data/tmp/multi_microbiology.sh -o <flow_cell_id>_jasen.csv --remote_dir /fs1/ryan/pipelines/jasen/bjorn/ --remote

Convert cgmlst.org target files to bed files

jasentool convert [-i INPUT_FILE [INPUT_FILE ...]] -o OUTPUT_FILE [-f OUT_FORMAT] [-a ACCESSION] [-h]

Converge tuberculosis mutation catlogues

jasentool converge --output_dir OUTPUT_DIR [--save_dbs]

Extract QC values after alignment

jasentool qc --sample_id SAMPLE_ID --bam_file BAM_FILE --reference REFERENCE -o OUTPUT_FILE [--bed_file BED_FILE] [--baits_file BAITS_FILE] [--cpus CPUS] [-h]