v1.3.0

Enhancements

• PR #24 - Cleaning up scripts and updating documents.
• PR #27 - Updating scripts so that irma_config files are compatible with AWS batch.
• PR #34 - Adding instrument type to instruments field when creating parquet and csv files.

Added

• PR #25 - If sourcepath flag is given, then it will use the sourcepath to point to the reference files, primer fastas and support files in all trimming modules, prepareIRMAjson and staticHTML. This flag is for if one can not place the entire repo in their working directory.
• PR #29 - Adding a custom_irma_config flag that allows user to pass a custom irma config to be passed to the pipeline for IRMA assembly.
• PR #30 - Adding a qc_settings flag that allows user to pass a custom qc pass/fail yaml to be passed to the pipeline to specify desired qc standards. Added Error handling.

Fixed

• PR #36 - Hot fix of paths broken by updated code

Dependencies

• PR #33 - Scipts and container cdcgov/mira-nf:python3.10-alpine are updated to contain new changes.

Deprecated

• PR #31 - renamed --irma_config flag to --irma_module and updated documentation. Added checkmiraversion.nf and checkmiraversion.py to check if users local version of MIRA-NF is up to date. Prints in stdout and email.

Parameter Changes

Old parameter	New parameter
	--sourcepath
	--irma_custom_config
--irma_config	--irma_module