v2.0.0 - 03.09.2026

• Amanda Sullivan
• Sam Wiley
• Ben Rambo-Martin

Associated Tags

Nextclade Tags Used

Enhancements

Added

• PR #76 - added both the find_variants_of_interest module that can be run as a part of analysis and the find_variants_of_interest workflow that run the the workflow described here.
• PR #82 - added a check_version flag that can be set to false so that MIRA-NF can be run with docker without internet. Default is set to true.
• PR #84 - added IRMA-core's standalone sampler module for subsampling single and paired-read .fastq files, replacing BBTools' reformat.sh.
• PR #88 - Added filtering to a single subtype for the variants_of_interest and positions_of_intrest outputs if the virus flu (as "INFLUENZA") is passed to the program.
• PR #94 - Subtype in the summary report for all viruses now.
• PR #94 - Added custom_runid flag to allow the user to pass a custom runid used to name outputs files. Otherwise the run folder name will be striped from runpath and used to name outputs.
• PR #95 - Added arm64 profiles for improved compatibilaty.
• PR #96 - Added Nextclade subworkflow that gets a nextclade database base on subtpye (and segment for flu) and runs nextclade when the --nextclade flag is used.
• PR #97 - Updated nf-core template to v3.3.2 and fixed formatting and whitespace issues.
• PR #98 - replaced alleles.json with minor_variants.json - will break MIRA GUI until updated
• PR #107 - add in github actions for pipeline testing and linting
• PR #114 - github action to chack that the nexclade tags are the most recent version

Fixed

• PR #77 - Update the nextflow schema with nf-core v3.2.0. Pipeline passing lint with nf-core v3.2.0 now.
• PR #85 - replaced findchemistryi.py and findchemistryo.py with findchemistry.rs from mira-oxide.
• PR #90 - Bug squash. Fix "MissingMissing" subtype in mira_summary report.
• PR #98 - reading in the allAlleles.txt files for the all_alleles.parq now - may break schemas

Dependencies

• PR #96 - new container nextstrain/nextclade:3.18.1 for running nexclade.
• PR #98 - updating mira-oxide container to v1.4.0
• PR #98 - removing the use of the cdcgov/mira-nf:python3.10-alpine container
• PR #118 - bumping nextclade container version to 3.19.0

Deprecated

• PR #84 - Removed BBTools reformat.sh for subsampling.
• PR #92 - replaced checkmiraversion.py with checkmiraversion.rs from mira-oxide.
• PR #94 - replaced prepareIRMAjson.py, irma2pandas.py, dais2pandas.py parquet_maker.py and extract_subtypes.py with prepare-mira-report from mira-oxide.
• PR #94 - replaced prepareirmajson.nf, statichtml.nf, parquetmaker.nf and addflusubtype.nf with preparemirareports.nf and preparemirareportswithparq.nf.
• PR #94 - replaced the reformat_tables flag with the parquet_files flag. CSV files now automatically generate and the parquet_files flag will iniate the generation of parquet files.
• PR #94 - No longer creating XSLX files in the mira-reports folder. CSV files are always geenrated to replace them.
• PR #98 - No longer making alleles.json or all_alleles.csv
• PR #98 - minor_variants.csv and minor_variants.parq no longer filtered to frequency of 0.05
• PR #98 - the minor_indel_count column has been removed from summary.csv, summary.json and summary.parq - may break schemas

Parameter Changes

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.

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 - 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 - 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 - 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 - 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

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 - 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

Enhancements

Added

Fixed

• PR #39 - Hot fix csv file format

Dependencies

Deprecated

Parameter Changes