v1.6.1

v1.6.1 - 06.04.2025

• Amanda Sullivan
• Sam Wiley
• Ben Rambo-Martin

Enhancements

Added

-PR #70 - adding docker version tracking

Fixed

-PR #72 - fix a polyg trimming bug in irma-core trimmer

Dependencies

-PR #73 - updating the IRMA container to v1.3.0

Deprecated

v1.6.0 - 05.21.2025

Credits

• Amanda Sullivan
• Sam Wiley
• Kristine Lacek
• Reina Chau
• Ben Rambo-Martin

Enhancements

Added

• PR #55 - Added new references (N4, N5 and N6) got DAIS-ribosome and update container.
• PR #66 - Added the ability to do custom primer trimming with the Flu-Illumina module

Fixed

• PR #53 - Fix error thrown when output directory and input directory have the same name. Address (issues #53)
• PR #56 - Minor spelling corrections, including a fix for parsing user-provided input for artic primers files in prepilluminareads.nf

Dependencies

• PR #54, PR #59 and PR #66- Added IRMA-core's standalone trimmer module for handling barcode, primer, and hard trimming for prepping ONT and Illumina reads, replacing BBDuk and cutadapt

Deprecated

• PR #54 - Removed cutadapt for hard trimming reads.
• PR #59 - Removed BBDuk for handling barcode and primer trimming of reads.
• PR #66 - Only performing the staging of Illumina fastq files for the standard (AWS) profile. It was removed for all other profiles.

v1.6.0-dockstore

What's Changed

• Add blast by @mandysulli in #52
• New na refs and bump DAIS version by @kristinelacek in #55
• Spelling fixes by @samcwiley in #56
• 51 start integration of trimmer into mira nf by @samcwiley in #54
• Zcat fix by @samcwiley in #58
• Remove BBDuk and combine left and right RSV and SC2 Illumina Primer Trimming by @samcwiley in #59
• add fourth dais output gen file for KF future compatibility by @kristinelacek in #60
• Expand dais refs prerelease by @kristinelacek in #62
• Add flu primers by @mandysulli in #66
• Update doc by @mandysulli in #68
• Dev by @mandysulli in #67
• Updating versions by @mandysulli in #69
• Dockstore by @nbx0 in #70

New Contributors

• @samcwiley made their first contribution in #56
• @nbx0 made their first contribution in #70

Full Changelog: v1.5.0...v1.6.0-dockstore

v1.6.0

v1.6.0 - 05.21.2025

Credits

• Amanda Sullivan
• Sam Wiley
• Kristine Lacek
• Reina Chau
• Ben Rambo-Martin

Enhancements

Added

• PR #55 - Added new references (N4, N5 and N6) got DAIS-ribosome and update container.
• PR #66 - Added the ability to do custom primer trimming with the Flu-Illumina module

Fixed

• PR #53 - Fix error thrown when output directory and input directory have the same name. Address (issues #53)
• PR #56 - Minor spelling corrections, including a fix for parsing user-provided input for artic primers files in prepilluminareads.nf

Dependencies

• PR #54, PR #59 and PR #66- Added IRMA-core's standalone trimmer module for handling barcode, primer, and hard trimming for prepping ONT and Illumina reads, replacing BBDuk and cutadapt

Deprecated

• PR #54 - Removed cutadapt for hard trimming reads.
• PR #59 - Removed BBDuk for handling barcode and primer trimming of reads.
• PR #66 - Only performing the staging of Illumina fastq files for the standard (AWS) profile. It was removed for all other profiles.

v1.5.0

v1.5.0 - 2025.04.02

Credits

• Amanda Sullivan
• Reina Chau

Enhancements

Added

Fixed

• PR #50 - Updated containers to work with docker, local profiles better.

Dependencies

Deprecated

v1.4.3

v1.4.3 - 2025.03.31

Credits

• Amanda Sullivan

Enhancements

Added

Fixed

• PR #49 - fixed binding to dais ribosome containers with docker profile.

Dependencies

Deprecated

v1.4.2

v1.4.2 - 2025.03.31

Credits

• Amanda Sullivan
• Kristine Lacek

Enhancements

Added

Fixed

• PR #48 - fixed the docker profile in the nextflow.config.

Dependencies

• PR #45 - Updated DAIS ribosome references to include translated A/Astrakhan N8 reference for compatibility with DAIS ribosome 1.1.5.

Deprecated

v1.4.1

v1.4.1

Credits

• Amanda Sullivan

Enhancements

Added

• PR #44 - adding configs for other profiles. restore the base config to it's original settings to be used as a template for other config files.

Fixed

• PR #43 - Fixing how the base base is extracted from the run path for naming parquet and cav files. Will now work with "." in the run name.

Dependencies

Deprecated

v1.4.0

v1.4.0 - 2025.01.23

Credits

• Amanda Sullivan

Enhancements

Added

• PR #41 - Adding in the subtype assigned by IRMA in the the summary csv for the flu modules. Only works for flu. Only adds them to the csv outputs.

Fixed

Dependencies

Deprecated

v1.3.1

Enhancements

Added

Fixed

• PR #39 - Hot fix csv file format

Dependencies

Deprecated

Parameter Changes

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