Fixes for 2.3.1 patch release

.github/workflows/ci.yml

@@ -110,6 +110,7 @@ jobs:
           - "--min_barcode_reads 10000"
           - "--min_guppyplex_reads 10000"
           - "--artic_minion_caller medaka --sequencing_summary false --fast5_dir false"
+          - "--artic_minion_caller medaka --sequencing_summary false --fast5_dir false --artic_minion_medaka_model r941_min_high_g360"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2

CHANGELOG.md

@@ -3,11 +3,11 @@
 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).
 
-## [Unpublished Version / DEV]
+## [[2.3.2](https://github.com/nf-core/viralrecon/releases/tag/2.3.2)] - 2022-02-21
 
 ### Enhancements & fixes
 
-### Parameters
+* [[#281](https://github.com/nf-core/viralrecon/issues/281)] - Nanopore medaka processing fails with error if model name, not model file, provided
 
 ## [[2.3.1](https://github.com/nf-core/viralrecon/releases/tag/2.3.1)] - 2022-02-15
 

modules.json

@@ -10,7 +10,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "artic/minion": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "cab399507bea60d90de6d7b296163210c371b693"
             },
             "bandage/image": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
@@ -79,7 +79,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "ivar/variants": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "cab399507bea60d90de6d7b296163210c371b693"
             },
             "kraken2/kraken2": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

nextflow.config

@@ -234,7 +234,7 @@ manifest {
     description     = 'Assembly and intrahost/low-frequency variant calling for viral samples'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '2.4dev'
+    version         = '2.3.2'
 }
 
 // Load modules.config for DSL2 module specific options

subworkflows/local/variants_ivar.nf

@@ -11,6 +11,7 @@ workflow VARIANTS_IVAR {
     take:
     bam                 // channel: [ val(meta), [ bam ] ]
     fasta               // channel: /path/to/genome.fasta
+    fai                 // channel: /path/to/genome.fai
     sizes               // channel: /path/to/genome.sizes
     gff                 // channel: /path/to/genome.gff
     bed                 // channel: /path/to/primers.bed
@@ -28,6 +29,7 @@ workflow VARIANTS_IVAR {
     IVAR_VARIANTS (
         bam,
         fasta,
+        fai,
         gff,
         params.save_mpileup
     )

workflows/illumina.nf

@@ -411,6 +411,7 @@ workflow ILLUMINA {
         VARIANTS_IVAR (
             ch_bam,
             PREPARE_GENOME.out.fasta,
+            PREPARE_GENOME.out.fai,
             PREPARE_GENOME.out.chrom_sizes,
             PREPARE_GENOME.out.gff,
             (params.protocol == 'amplicon' && params.primer_bed) ? PREPARE_GENOME.out.primer_bed : [],

workflows/nanopore.nf

@@ -308,6 +308,7 @@ workflow NANOPORE {
         PREPARE_GENOME.out.fasta,
         PREPARE_GENOME.out.primer_bed,
         ch_medaka_model.collect().ifEmpty([]),
+        params.artic_minion_medaka_model,
         params.artic_scheme,
         params.primer_set_version
     )