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

v1.2.0

Enhancements

• PR #10 - reformat the outputs structure
• PR #11 - changes the parquet_files flag to reformat_tables flag. This flag now reformats the report tables into parquet files and csv files.
• PR #12 - Restructure so that the readqc subworkflow only runs when the flag --read_qc is set to true. Otherwise FastQC and MultiQC will not run.
• PR #13 - creating and updating docker containers so that they contain no vulnerabilities.
• PR #14 - updating scripts and logs to reflect new changes.
• PR #16 - Continuing to update containers to containers with no vulnerabilities.
• PR #17 - Updating Java versions in containers.
• PR #18 - Merging all changes that allow MIRA-NF to run in both AWS-omics and on HPC's.
• PR #19 - Altering workflows to skip the subsampling process if a values greater than 0 is not provide using the subsample_reads flag
• PR #20 - Adding the ecr_registry parameter that allows a user to pass their ecr registry for AWS to the workflow.

Parameters

Old parameter	New parameter
--parquet_files	--reformat_tables
	--read_qc
	--ecr_registry

v1.1.0

This release has new features, flags and two new workflows: RSV-Illumina and RSV-ONT. For information on how use the new workflows, consult the README.md and usage.md. All changes were added to the CHANGELOGS.md