Merge branch 'dev' into multiple_DOI

nf-core · May 3, 2024 · 0a9746a · 0a9746a
2 parents fa0b60d + 3609acd
commit 0a9746a
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Showing 5 changed files with 18 additions and 4 deletions.
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -184,7 +184,7 @@ jobs:
           coverage report
           coverage xml
 
-      - uses: codecov/codecov-action@84508663e988701840491b86de86b666e8a86bed # v4
+      - uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be # v4
         with:
           files: coverage.xml
         env:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,7 @@
 - Shorten lines in pipeline template ([#2908](https://github.com/nf-core/tools/pull/2908))
 - Permanently activated pipeline-specific institutional configs support for all pipelines without need for manual intervention ([#2936](https://github.com/nf-core/tools/pull/2936))
 - Handles multiple DOIs + doi.org resolver from manifest.doi ([#2946](https://github.com/nf-core/tools/pull/2946))
+- Update included components ([#2949](https://github.com/nf-core/tools/pull/2949))
 
 ### Linting
 
@@ -63,6 +64,7 @@
 - Update gitpod/workspace-base Docker digest to 5aeb24f ([#2929](https://github.com/nf-core/tools/pull/2929))
 - Update pre-commit hook pre-commit/mirrors-mypy to v1.10.0 ([#2933](https://github.com/nf-core/tools/pull/2933))
 - Update GitHub Actions ([#2939](https://github.com/nf-core/tools/pull/2939))
+- Update codecov/codecov-action digest to 5ecb98a ([#2948](https://github.com/nf-core/tools/pull/2948))
 - Update gitpod/workspace-base Docker digest to 124f2b8 ([#2943](https://github.com/nf-core/tools/pull/2943))
 
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
+                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -26,7 +26,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {

diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf b/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf