Merge pull request #300 from heylf/dev

Fix to issue 299 and 297
nf-core · Mar 13, 2024 · d554870 · d554870
2 parents ae5b28b + e20e897
commit d554870
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Showing 7 changed files with 19 additions and 5 deletions.
diff --git a/.gitignore b/.gitignore
@@ -10,3 +10,4 @@ log/
 reports/
 testme.sh
 .nf-test*
+.vscode
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Change from pytests to nf-test ([#291](https://github.com/nf-core/scrnaseq/pull/291))
 - Update template to v2.13.1 ([#309](https://github.com/nf-core/scrnaseq/pull/309))
 - Update to kallisto|bustools v0.28.2 ([#294](https://github.com/nf-core/scrnaseq/pull/294))
+- Fix cellrangerarc matrix conversions and protocol selection ([#300](https://github.com/nf-core/scrnaseq/pull/300))
 
 ## v2.5.1
 

diff --git a/assets/protocols.json b/assets/protocols.json
@@ -30,6 +30,11 @@
             "protocol": "SC3Pv3"
         }
     },
+    "cellrangerarc": {
+        "auto": {
+            "protocol": "auto"
+        }
+    },
     "star": {
         "10XV1": {
             "protocol": "CB_UMI_Simple",

diff --git a/modules.json b/modules.json
@@ -22,7 +22,7 @@
                     },
                     "cellrangerarc/count": {
                         "branch": "master",
-                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
+                        "git_sha": "18e53e27cfeca5dbbfbeee675c05438dec68245f",
                         "installed_by": ["modules"]
                     },
                     "cellrangerarc/mkgtf": {
@@ -42,7 +42,7 @@
                     },
                     "gffread": {
                         "branch": "master",
-                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
+                        "git_sha": "b1b959609bda44341120aed1766329909f54b8d0",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {

diff --git a/modules/nf-core/cellrangerarc/count/main.nf b/modules/nf-core/cellrangerarc/count/main.nf
diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test
diff --git a/modules/nf-core/gffread/tests/nextflow-gff3.config b/modules/nf-core/gffread/tests/nextflow-gff3.config