Merge pull request #259 from nschcolnicov/updates

Updated modules and subworkflows
nf-core · Sep 17, 2024 · 8c8fec3 · 8c8fec3
2 parents d1c474c + ad66840
commit 8c8fec3
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Showing 14 changed files with 129 additions and 112 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -77,10 +77,12 @@ jobs:
  --shard ${{ matrix.shard }}/${{ env.SHARDS }} \
  --changed-since HEAD^ \
  --profile "+${{ matrix.profile }}" \
- --filter pipeline
+ --filter pipeline \
+ --junitxml=test.xml
 
  - name: Publish Test Report
  uses: mikepenz/action-junit-report@v3
  if: always() # always run even if the previous step fails
  with:
  report_paths: test.xml
+ annotate_only: true
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## 1.5.2dev (UNRELEASED)
 
+### `Changed`
+
+- [#253](https://github.com/nf-core/demultiplex/pull/256) Updated all modules and subworkflows, and added new bclconvert test profile.
+
 ## 1.5.1
 
 ### `Fixed`

diff --git a/modules.json b/modules.json
@@ -12,7 +12,7 @@
  },
  "bcl2fastq": {
  "branch": "master",
- "git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9",
+ "git_sha": "90b63cde0f838ca4da3a88a37a5309888cae97b9",
  "installed_by": ["bcl_demultiplex"]
  },
  "bclconvert": {
@@ -42,7 +42,7 @@
  },
  "fastqc": {
  "branch": "master",
- "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+ "git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5",
  "installed_by": ["modules"]
  },
  "fqtk": {
@@ -62,7 +62,7 @@
  },
  "multiqc": {
  "branch": "master",
- "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
+ "git_sha": "19ca321db5d8bd48923262c2eca6422359633491",
  "installed_by": ["modules"]
  },
  "seqtk/sample": {
@@ -86,7 +86,7 @@
  "nf-core": {
  "bcl_demultiplex": {
  "branch": "master",
- "git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9",
+ "git_sha": "a6e6bec1b1da613b89a6c0a3a46713f880cf5aca",
  "installed_by": ["subworkflows"]
  },
  "fastq_contam_seqtk_kraken": {
@@ -96,12 +96,12 @@
  },
  "utils_nextflow_pipeline": {
  "branch": "master",
- "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+ "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
  "installed_by": ["subworkflows"]
  },
  "utils_nfcore_pipeline": {
  "branch": "master",
- "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
+ "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
  "installed_by": ["subworkflows"]
  },
  "utils_nfvalidation_plugin": {

diff --git a/modules/nf-core/bcl2fastq/tests/main.nf.test b/modules/nf-core/bcl2fastq/tests/main.nf.test
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
diff --git a/subworkflows/nf-core/bcl_demultiplex/main.nf b/subworkflows/nf-core/bcl_demultiplex/main.nf
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config