Merge pull request #263 from nf-core/modules-updates

Update Modules
nf-core · Oct 3, 2024 · 3b2ef64 · 3b2ef64
2 parents 73df4a5 + b40ecc6
commit 3b2ef64
Show file tree

Hide file tree

Showing 46 changed files with 1,014 additions and 708 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
@@ -7,77 +7,77 @@
                 "nf-core": {
                     "bases2fastq": {
                         "branch": "master",
-                        "git_sha": "c651992bf8425fecefe14085ff486f42172cba77",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "bcl2fastq": {
                         "branch": "master",
-                        "git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["bcl_demultiplex"]
                     },
                     "bclconvert": {
                         "branch": "master",
-                        "git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["bcl_demultiplex"]
                     },
                     "cellranger/mkfastq": {
                         "branch": "master",
-                        "git_sha": "61123e49c6034920eb6f312ad71e4815a7853257",
+                        "git_sha": "a90a8863a3408e15d5a339b06413e57cf9ca9860",
                         "installed_by": ["modules"]
                     },
                     "checkqc": {
                         "branch": "master",
-                        "git_sha": "337bc962d03c2e08a728c9bf731a2148e323e731",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "falco": {
                         "branch": "master",
-                        "git_sha": "a236d2c2ec9e68db9b8501105d804acb359552b5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "fqtk": {
                         "branch": "master",
-                        "git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
-                        "git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["fastq_contam_seqtk_kraken"]
                     },
                     "md5sum": {
                         "branch": "master",
-                        "git_sha": "1164836d4d3922ab937865b17086485f0f472748",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
+                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
                         "installed_by": ["modules"]
                     },
                     "seqtk/sample": {
                         "branch": "master",
-                        "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["fastq_contam_seqtk_kraken"]
                     },
                     "sgdemux": {
                         "branch": "master",
-                        "git_sha": "574074e6ea2497b53df1f226473a8c71524af0d0",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }
                 }
@@ -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/bases2fastq/meta.yml b/modules/nf-core/bases2fastq/meta.yml