Recent Releases of mira-nf
mira-nf - v1.6.1
v1.6.1 - 06.04.2025
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
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
articprimers files inprepilluminareads.nf
Dependencies
- PR #54, PR #59 and PR #66- Added IRMA-core's standalone
trimmermodule for handling barcode, primer, and hard trimming for prepping ONT and Illumina reads, replacing BBDuk and cutadapt
Deprecated
- PR #54 - Removed
cutadaptfor 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.
- Nextflow
Published by mandysulli 9 months ago
mira-nf - v1.6.0-dockstore
What's Changed
- Add blast by @mandysulli in https://github.com/CDCgov/MIRA-NF/pull/52
- New na refs and bump DAIS version by @kristinelacek in https://github.com/CDCgov/MIRA-NF/pull/55
- Spelling fixes by @samcwiley in https://github.com/CDCgov/MIRA-NF/pull/56
- 51 start integration of trimmer into mira nf by @samcwiley in https://github.com/CDCgov/MIRA-NF/pull/54
- Zcat fix by @samcwiley in https://github.com/CDCgov/MIRA-NF/pull/58
- Remove BBDuk and combine left and right RSV and SC2 Illumina Primer Trimming by @samcwiley in https://github.com/CDCgov/MIRA-NF/pull/59
- add fourth dais output gen file for KF future compatibility by @kristinelacek in https://github.com/CDCgov/MIRA-NF/pull/60
- Expand dais refs prerelease by @kristinelacek in https://github.com/CDCgov/MIRA-NF/pull/62
- Add flu primers by @mandysulli in https://github.com/CDCgov/MIRA-NF/pull/66
- Update doc by @mandysulli in https://github.com/CDCgov/MIRA-NF/pull/68
- Dev by @mandysulli in https://github.com/CDCgov/MIRA-NF/pull/67
- Updating versions by @mandysulli in https://github.com/CDCgov/MIRA-NF/pull/69
- Dockstore by @nbx0 in https://github.com/CDCgov/MIRA-NF/pull/70
New Contributors
- @samcwiley made their first contribution in https://github.com/CDCgov/MIRA-NF/pull/56
- @nbx0 made their first contribution in https://github.com/CDCgov/MIRA-NF/pull/70
Full Changelog: https://github.com/CDCgov/MIRA-NF/compare/v1.5.0...v1.6.0-dockstore
- Nextflow
Published by nbx0 9 months ago
mira-nf - v1.6.0
v1.6.0 - 05.21.2025
Credits
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
articprimers files inprepilluminareads.nf
Dependencies
- PR #54, PR #59 and PR #66- Added IRMA-core's standalone
trimmermodule for handling barcode, primer, and hard trimming for prepping ONT and Illumina reads, replacing BBDuk and cutadapt
Deprecated
- PR #54 - Removed
cutadaptfor 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.
- Nextflow
Published by mandysulli 9 months ago
mira-nf - v1.4.2
v1.4.2 - 2025.03.31
Credits
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
- Nextflow
Published by mandysulli 11 months ago
mira-nf - v1.4.1
v1.4.1
Credits
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
- Nextflow
Published by mandysulli about 1 year ago
mira-nf - 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 customirmaconfig 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 --irmaconfig flag to --irmamodule 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 |
- Nextflow
Published by mandysulli about 1 year ago
mira-nf - v1.2.0
Enhancements
- PR #10 - reformat the outputs structure
- PR #11 - changes the parquetfiles flag to reformattables 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_qcis 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 |
- Nextflow
Published by mandysulli over 1 year ago