Post-run analysis

Subcommands for querying and analysing results after JASEN runs.

find

jasentool find --query <QUERY> [--query ...] --db-name <DB> --db-collection <COLLECTION>
               (--output-file <FILE> | --output-dir <DIR>)
               [--address <URI>] [--prefix <PREFIX>] [--combined-output]

Argument	Required	Default	Description
-q/--query	Yes	—	One or more sample queries
--db-name	Yes	—	MongoDB database name
--db-collection	Yes	—	MongoDB collection name
--output-file/--output-dir	Yes (one)	—	Output file or directory
--address/--uri	No	mongodb://localhost:27017/	MongoDB host address
--prefix	No	jasentool_results_	Prefix for output files
--combined-output	No	False	Combine all outputs into one file

Example

jasentool find \
  --query MySample \
  --db-name mydb \
  --db-collection samples \
  --output-file results.json

identify-missing

jasentool identify-missing --output-file <FILE> --db-name <DB> --db-collection <COLLECTION>
                            [-i <FILE> [...]]
                            [--analysis-dir <DIR>] [--restore-dir <DIR>] [--restore-file <FILE>]
                            [--missing-log <FILE>] [--assay <ASSAY>] [--platform <PLATFORM>]
                            [--sample-sheet] [--alter-sample-id]

Argument	Required	Default	Description
-o/--output-file	Yes	—	Output file path
--db-name	Yes	—	MongoDB database name
--db-collection	Yes	—	MongoDB collection name
-i/--input-file	No	—	Input filepath(s)
--analysis-dir	No	—	Analysis results directory containing JASEN results
--restore-dir	No	/fs2/seqdata/restored	Directory for restored spring files
--restore-file	No	—	Output bash shell script (.sh)
--missing-log	No	missing_samples.log	File to log missing samples
--assay	No	jasen-saureus-dev	JASEN assay name
--platform	No	illumina	Sequencing platform
--sample-sheet	No	False	Use sample sheet input
--alter-sample-id	No	False	Alter sample ID to LIMS ID + sequencing run

Example

jasentool identify-missing \
  --output-file missing.json \
  --db-name mydb \
  --db-collection samples \
  --analysis-dir /fs1/results/jasen

validate-pipelines

jasentool validate-pipelines (--input-file <FILE> [...] | --input-dir <DIR>)
                              (--output-file <FILE> | --output-dir <DIR>)
                              --db-name <DB> --db-collection <COLLECTION>
                              [--address <URI>] [--prefix <PREFIX>]
                              [--combined-output] [--generate-matrix]

Argument	Required	Default	Description
-i/--input-file	Yes (or --input-dir)	—	Input filepath(s)
--input-dir	Yes (or --input-file)	—	Directory containing sample files
--output-file/--output-dir	Yes (one)	—	Output file or directory
--db-name	Yes	—	MongoDB database name
--db-collection	Yes	—	MongoDB collection name
--address/--uri	No	mongodb://localhost:27017/	MongoDB host address
--prefix	No	jasentool_results_	Prefix for output files
--combined-output	No	False	Combine all outputs into one file
--generate-matrix	No	False	Generate cgMLST matrix

Example

jasentool validate-pipelines \
  --input-dir /new/results \
  --output-dir /validation/output \
  --db-name mydb \
  --db-collection samples \
  --generate-matrix