Merge branch 'CW-1015' into 'dev'

Add enum basecallers CW-1015 See merge request epi2melabs/workflows/wf-bacterial-genomes!55
epi2me-labs · Feb 7, 2023 · 15fecf5 · 15fecf5
2 parents db32702 + 9a99232
commit 15fecf5
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Showing 4 changed files with 23 additions and 3 deletions.
diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,5 @@ nextflow
 template-workflow
 .*.swp
 .*.swo
+*.pyc
+*.pyo
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 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).
 
-## [unreleased]
+## [v0.2.11]
 ### Changed
 - `--basecall_cfg` is now used to determine suitable Medaka model, alternatively provide the name of a model with `--medaka_consensus_model` and `--medaka_variant_model` to override automatic selection.
 

diff --git a/nextflow.config b/nextflow.config
@@ -47,7 +47,7 @@ manifest {
     description     = 'Assembly, variant calling, and annotation of bacterial genomes.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=20.10.0'
-    version         = 'v0.2.10'
+    version         = 'v0.2.11'
 }
 
 epi2melabs {

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -39,7 +39,25 @@
                 "basecaller_cfg": {
                     "type": "string",
                     "description": "Name of the model that was used to basecall signal data, used to select an appropriate Medaka model.",
-                    "help_text": "The basecaller configuration is used to automatically select the appropriate Medaka model. Refer to the [model table on the Dorado repository for selecting a simplex basecalling model](https://github.com/nanoporetech/dorado#available-basecalling-models). The automatic selection can be overridden with the 'medaka_variant_model' and 'medaka_consensus_model' parameters."
+                    "help_text": "The basecaller configuration is used to automatically select the appropriate Medaka model. The automatic selection can be overridden with the 'medaka_variant_model' and 'medaka_consensus_model' parameters. The model list only shows models that are compatible with this workflow.",
+                    "default": "dna_r10.4.1_e8.2_400bps_hac",
+                    "enum": [
+                        "dna_r10.4.1_e8.2_400bps_hac@v3.5.2",
+                        "dna_r10.4.1_e8.2_400bps_sup@v3.5.2",
+                        "dna_r9.4.1_e8_fast@v3.4",
+                        "dna_r9.4.1_e8_hac@v3.3",
+                        "dna_r9.4.1_e8_sup@v3.3",
+                        "dna_r10.4.1_e8.2_400bps_hac_prom",
+                        "dna_r9.4.1_450bps_hac_prom",
+                        "dna_r10.3_450bps_hac",
+                        "dna_r10.3_450bps_hac_prom",
+                        "dna_r10.4.1_e8.2_260bps_hac",
+                        "dna_r10.4.1_e8.2_260bps_hac_prom",
+                        "dna_r10.4.1_e8.2_400bps_hac",
+                        "dna_r9.4.1_450bps_hac",
+                        "dna_r9.4.1_e8.1_hac",
+                        "dna_r9.4.1_e8.1_hac_prom"
+                    ]
                 },
                 "analyse_unclassified": {
                     "type": "boolean",