Merge pull request #150 from FloWuenne/unicycler_nfcore

Replace local unicycler module with nf-core module + bump version
nf-core · Jun 28, 2024 · 03f0dc8 · 03f0dc8
2 parents b3eda16 + e922812
commit 03f0dc8
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Showing 11 changed files with 273 additions and 14 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,20 @@
 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).
 
+## v2.4.0 nf-core/bacass
+
+### `Changed`
+
+- [#150](https://github.com/nf-core/bacass/pull/150) Replace local unicycler module with nf-core module + bump version
+
+### `Added`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v2.3.1 nf-core/bacass: "Navy Iron Oyster" 2024/06/24
 
 ### `Changed`

diff --git a/conf/test.config b/conf/test.config
@@ -23,7 +23,6 @@ params {
     input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv'
 
     // some extra args to speed tests up
-    unicycler_args  = "--no_correct --no_pilon"
     prokka_args     = " --fast"
     assembly_type   = 'short'
     skip_pycoqc     = true

diff --git a/conf/test_dfast.config b/conf/test_dfast.config
@@ -23,7 +23,6 @@ params {
     input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv'
 
     // some extra args to speed tests up
-    unicycler_args  = "--no_correct --no_pilon"
     annotation_tool = 'dfast'
     assembly_type   = 'short'
     skip_pycoqc     = true

diff --git a/modules.json b/modules.json
@@ -92,6 +92,11 @@
                         "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
                         "installed_by": ["modules"]
                     },
+                    "unicycler": {
+                        "branch": "master",
+                        "git_sha": "5f65b5398f3fe4b8d51d77ed90b0a8cd8c89bba7",
+                        "installed_by": ["modules"]
+                    },
                     "untar": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",

diff --git a/modules/local/unicycler/environment.yml → modules/nf-core/unicycler/environment.yml b/modules/local/unicycler/environment.yml → modules/nf-core/unicycler/environment.yml
diff --git a/modules/local/unicycler/main.nf → modules/nf-core/unicycler/main.nf b/modules/local/unicycler/main.nf → modules/nf-core/unicycler/main.nf
diff --git a/modules/nf-core/unicycler/meta.yml b/modules/nf-core/unicycler/meta.yml
diff --git a/modules/nf-core/unicycler/tests/main.nf.test b/modules/nf-core/unicycler/tests/main.nf.test
diff --git a/modules/nf-core/unicycler/tests/main.nf.test.snap b/modules/nf-core/unicycler/tests/main.nf.test.snap
diff --git a/modules/nf-core/unicycler/tests/tags.yml b/modules/nf-core/unicycler/tests/tags.yml
diff --git a/workflows/bacass.nf b/workflows/bacass.nf
@@ -27,7 +27,7 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
 // MODULE: Local to the pipeline
 //
 include { PYCOQC                    } from '../modules/local/pycoqc'
-include { UNICYCLER                 } from '../modules/local/unicycler'
+include { UNICYCLER                 } from '../modules/nf-core/unicycler/main'
 include { NANOPOLISH                } from '../modules/local/nanopolish'
 include { MEDAKA                    } from '../modules/local/medaka'
 include { KRAKEN2_DB_PREPARATION    } from '../modules/local/kraken2_db_preparation'