ONT and Illumina Variant Processing Cleanup

CHANGELOG.md

@@ -3,6 +3,49 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v1.3.0] - 2026-07-06
+
+Code cleanup, exposed nanopore frameshift quality parameter, added excess ambiguity warning, artic version bump to `v1.10.3`, and clair3 version bump from `v1.2.0` to `v2.0.2`.
+
+Big Note: The Clair3 `v1.2.0` models have to be converted to the new format. The update to `artic` will pull these new versions by default if you are providing a `--model <model name>` name on the command line. If you are using a local model you'll have to grab the new version. More info is available in [clair3's docs](https://github.com/HKU-BAL/clair3#pre-trained-models). No consensus variant output changes noted in the test datasets with this update.
+
+### `Added`
+
+- `--min_frameshift_qual_c3` arg to adjust the minimum cutoff for a frameshift variant to be called for nanopore data [PR #43](https://github.com/phac-nml/measeq/pull/43)
+
+  - Default is the same at `30`
+
+- Added an excess ambiguity warning [PR #43](https://github.com/phac-nml/measeq/pull/43)
+
+  - `>=5` sites for Illumina by default
+  - `>=10` sites for Nanopore by default
+  - Its configurable in the `modules.json` file
+
+- Added nextflow channel check to make sure that the input model folder has a `.pt` extension file required [PR #43](https://github.com/phac-nml/measeq/pull/43)
+
+### `Adjusted`
+
+- Renamed the VCF parsing scripts to make them easier to distinguish [PR #43](https://github.com/phac-nml/measeq/pull/43)
+
+  - process_nanopore_vcf.py
+  - process_illumina_vcf.py
+
+- Illumina VCF parsing adjusted to better handle complex sites where an INDEL and a SNP are called with the SNP being the final call [PR #43](https://github.com/phac-nml/measeq/pull/43)
+
+  - No consensus output differences
+  - Adjusts the calculation for mixed sites so it rem
+  - Adjusts the need to split ambiguous sites from consensus sites in VCF outputs for downstream processing
+    - New filename for the illumina consensus variants file `.consensus.norm.vcf.gz` instead of `.processed.norm.vcf.gz`
+
+- Split out the `artic` subcommands into their own folders to better match the nextflow best practices [PR #43](https://github.com/phac-nml/measeq/pull/43)
+- Artic updated to `v1.10.3` in all spots that were `v1.8.5` [PR #43](https://github.com/phac-nml/measeq/pull/43)
+- Clair3 updated to `v2.0.2` [PR #43](https://github.com/phac-nml/measeq/pull/43)
+
+## Removed
+
+- Intermediate BCFTools consensus step in illumina workflow that applied ambiguous sites [PR #43](https://github.com/phac-nml/measeq/pull/43)
+  - Ambiguous sites now have correct genotypes associated and can just run the command once
+
 ## [v1.2.0] - 2026-05-20
 
 Update to enable users to map reads with Bowtie 2 instead of BWAMem as an optional parameter and use Artic primers as default. Add in parameter to better control ONT variant masking

assets/methods_description_template.yml

@@ -3,7 +3,7 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "phac-nml/measeq Methods Description"
 section_href: "https://github.com/phac-nml/measeq"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
+## Unused
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>

assets/subpage_sample.Rmd

@@ -241,7 +241,7 @@ if (file.exists(var_f)) {
     datatable(rownames = FALSE,
       caption = htmltools::tags$caption(
         style = 'caption-side: top',
-        htmltools::strong('Table III: '), 'Consensus Variant Summary Table. VCF-based summary table of the variants found in the final consensus sequence. The "Type" column displays more information on the variant call such as if the site was masked (Nanopore) or an IUPAC base (Illumina).'
+        htmltools::strong('Table III: '), 'Consensus Variant Summary Table. VCF-based summary table of the variants found in the final consensus sequence. The "Type" column displays more information on the variant call such as if the site was masked (Nanopore) or an ambiguous base (Illumina).'
       ),
       options = list(
         pageLength = 10,