Merge pull request #288 from nf-core/module-update

Fix cellranger and bump version to 2.5.1

.devcontainer/devcontainer.json

@@ -18,11 +18,11 @@
                 "python.linting.flake8Path": "/opt/conda/bin/flake8",
                 "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
                 "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.linting.pylintPath": "/opt/conda/bin/pylint",
             },
 
             // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
-    }
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
+        },
+    },
 }

.github/workflows/ci.yml

@@ -26,13 +26,13 @@ jobs:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
-        profile:
-          [
+        profile: [
             "test,docker --aligner alevin",
             "test,docker --aligner kallisto",
             "test,docker --aligner star",
-            "test,docker --aligner cellranger -stub",
-            "test,docker --aligner universc -stub",
+            "test,docker --aligner cellranger",
+            # "test,docker --aligner cellrangerarc", // this currently lacks a suitable test profile, see issue https://github.com/nf-core/scrnaseq/issues/290
+            # "test,docker --aligner universc", // this is broken, see issue https://github.com/nf-core/scrnaseq/issues/289
           ]
     steps:
       - name: Free some space

CHANGELOG.md

@@ -3,6 +3,11 @@
 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).
 
+## v2.5.1
+
+- Fix that cellranger workflow couldn't be run and enable CI for this workflow ([#288](https://github.com/nf-core/scrnaseq/pull/288)).
+- Update modules ([#288]()https://github.com/nf-core/scrnaseq/pull/288).
+
 ## v2.5.0 - 2024-01-02
 
 - Update template to v2.11.1 ([#279](https://github.com/nf-core/scrnaseq/pull/279))

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/tree/dev" target="_blank">nf-core/scrnaseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/releases/tag/2.5.1" target="_blank">nf-core/scrnaseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/scrnaseq/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/scrnaseq/2.5.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-scrnaseq-methods-description":
     order: -1000

modules.json

@@ -20,24 +20,39 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
+                    "cellrangerarc/count": {
+                        "branch": "master",
+                        "git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
+                        "installed_by": ["modules"]
+                    },
+                    "cellrangerarc/mkgtf": {
+                        "branch": "master",
+                        "git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
+                        "installed_by": ["modules"]
+                    },
+                    "cellrangerarc/mkref": {
+                        "branch": "master",
+                        "git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
+                        "installed_by": ["modules"]
+                    },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
+                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
+                        "git_sha": "617777a807a1770f73deb38c80004bac06807eef",
                         "installed_by": ["modules"]
                     },
                     "gffread": {
                         "branch": "master",
-                        "git_sha": "a2d6c3082c5c44b4155a3246daff36701ee49af8",
+                        "git_sha": "b8858b10356b87db4325341872816f9672541b7b",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
                         "installed_by": ["modules"]
                     },
                     "kallistobustools/count": {
@@ -52,7 +67,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
+                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {

modules/local/mtx_to_seurat.nf

@@ -20,9 +20,9 @@ process MTX_TO_SEURAT {
     script:
     def aligner = params.aligner
     if (params.aligner in [ 'cellranger', 'cellrangerarc' ]) {
-        matrix   = "filtered_feature_bc_matrix/matrix.mtx.gz"
-        barcodes = "filtered_feature_bc_matrix/barcodes.tsv.gz"
-        features = "filtered_feature_bc_matrix/features.tsv.gz"
+        matrix   = "matrix.mtx.gz"
+        barcodes = "barcodes.tsv.gz"
+        features = "features.tsv.gz"
     } else if (params.aligner == "kallisto") {
         matrix   = "*count/counts_unfiltered/*.mtx"
         barcodes = "*count/counts_unfiltered/*.barcodes.txt"