Merge branch 'CW-1708-windows-primer-path' into 'dev'

CW-1708-windows-primer-scheme-fix Closes CW-1708 See merge request epi2melabs/workflows/wf-artic!128
epi2me-labs · Mar 10, 2023 · 12b22c3 · 12b22c3
2 parents baa2103 + 3291a5b
commit 12b22c3
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Showing 5 changed files with 19 additions and 17 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -18,7 +18,7 @@ repos:
         additional_dependencies:
           - epi2melabs
   - repo: https://github.com/pycqa/flake8
-    rev: 3.7.9
+    rev: 5.0.4
     hooks:
       - id: flake8
         pass_filenames: false

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,13 +4,19 @@ 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).
 
+## [v0.3.23]
+### Changed
+- medaka bumped to 1.7.2 (np-artic bump to 1.3.0_19)
+### Added
+- medaka models for kit14 - R10.4.1
+### Fixed
+- scheme directory bug in labs/windows (https://github.com/epi2me-labs/wf-artic/issues/73)
+
 ## [v0.3.22]
 ### Changed
 - workflow-glue python psuedo package
 - pangolin to 4.2
 - nextclade to 2.11.0
-### Fixed
-- scheme directory bug in labs/windows (https://github.com/epi2me-labs/wf-artic/issues/73)
 ### Removed
 - spike-seq primer schemes
 - telemtry generation

diff --git a/main.nf b/main.nf
@@ -543,13 +543,15 @@ workflow {
           params._max_len = params.max_len
           params.remove('max_len')
       }
-
-      schemes = """./data/${params.scheme_dir}"""
+
+
+      scheme_dir_name = "primer_schemes"
+      schemes = """./data/${scheme_dir_name}"""
       scheme_dir = file(projectDir.resolve(schemes), type:'file', checkIfExists:true)
-      primers_path = """./data/${params.scheme_dir}/${params.scheme_name}/${params.scheme_version}/${params.scheme_name}.scheme.bed"""
+      primers_path = """./data/${scheme_dir_name}/${params.scheme_name}/${params.scheme_version}/${params.scheme_name}.scheme.bed"""
       primers = file(projectDir.resolve(primers_path), type:'file', checkIfExists:true)
 
-      reference_path = """./data/${params.scheme_dir}/${params.scheme_name}/${params.scheme_version}/${params.scheme_name}.reference.fasta"""
+      reference_path = """./data/${scheme_dir_name}/${params.scheme_name}/${params.scheme_version}/${params.scheme_name}.reference.fasta"""
       reference = file(projectDir.resolve(reference_path),type:'file', checkIfExists:true)
 
     } else {

diff --git a/nextflow.config b/nextflow.config
@@ -27,7 +27,6 @@ params {
     report_depth = 100
     medaka_model = "r941_min_hac_variant_g507"
     scheme_name = "SARS-CoV-2"
-    scheme_dir = "primer_schemes"
     scheme_version = "ARTIC/V3"
     list_schemes = false
     custom_scheme = null
@@ -59,7 +58,7 @@ params {
           "--fastq test_data/sars-samples-demultiplexed",
           "--sample_sheet test_data/sample_sheet.csv"
       ]
-      container_sha = 'sha1ea69f663b444a23374dc89c85d5c81cf8aa60d9'
+      container_sha = 'sha6085f371ad3edd59bb7d795c3721f12b434c8c78'
       nextclade_sha = 'shaede3ca9a1b17c2a1d0696ef7ff8503ec167d5df9'
       pangolin_sha = 'sha1266e6040bf6e9f02e569f0eba5011a17d47f7aa'
   }
@@ -72,7 +71,7 @@ manifest {
     description     = 'Run the ARTIC SARS-CoV-2 methodology on multiplexed MinION, GridION, and PromethION data.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=20.10.0'
-    version         = 'v0.3.22'
+    version         = 'v0.3.23'
 }
 
 epi2melabs {

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -70,13 +70,6 @@
                     "format": "path",
                     "description": "Path to a custom scheme.",
                     "help_text": "If you have a custom primer scheme you can enter the details here. This must be the full path to the directory containing your appropriately named scheme bed and fasta files; <SCHEME_NAME>.bed and <SCHEME_NAME>.fasta. More details [here](https://labs.epi2me.io/ont-midnight-scheme-update/)."
-                },
-                "scheme_dir": {
-                    "type": "string",
-                    "format": "path",
-                    "description": "Path to primer scheme.",
-                    "default": "primer_schemes",
-                    "hidden": true
                 }
             }
         },
@@ -234,6 +227,8 @@
                     "description": "Medaka model name.",
                     "help_text": "The correct medaka model to use is determined by the Guppy basecaller version, see [Medaka Models](https://github.com/nanoporetech/medaka#models) for more information.",
                     "enum": [
+                        "r1041_e82_400bps_hac_variant_g615",
+                        "r1041_e82_400bps_sup_variant_g615",
                         "r103_fast_variant_g507",
                         "r103_hac_variant_g507",
                         "r103_prom_variant_g3210",