Update modules and fix linting

nf-core · Mar 7, 2024 · 4203d14 · 4203d14
1 parent 66bbb99
commit 4203d14
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Showing 10 changed files with 196 additions and 10 deletions.
diff --git a/lib/WorkflowScrnaseq.groovy → lib/Utils.groovy b/lib/WorkflowScrnaseq.groovy → lib/Utils.groovy
diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "cellranger/count": {
                         "branch": "master",
-                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
+                        "git_sha": "a2dfd9a0b2e192243695711c723d652959de39fc",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkgtf": {
@@ -35,11 +35,6 @@
                         "git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
                         "installed_by": ["modules"]
                     },
-                    "custom/dumpsoftwareversions": {
-                        "branch": "master",
-                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
-                        "installed_by": ["modules"]
-                    },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",

diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf
diff --git a/modules/nf-core/cellranger/count/meta.yml b/modules/nf-core/cellranger/count/meta.yml
diff --git a/modules/nf-core/cellranger/count/templates/cellranger_count.py b/modules/nf-core/cellranger/count/templates/cellranger_count.py
diff --git a/modules/nf-core/cellranger/count/tests/main.nf.test b/modules/nf-core/cellranger/count/tests/main.nf.test
diff --git a/modules/nf-core/cellranger/count/tests/main.nf.test.snap b/modules/nf-core/cellranger/count/tests/main.nf.test.snap
diff --git a/modules/nf-core/cellranger/count/tests/nextflow.config b/modules/nf-core/cellranger/count/tests/nextflow.config
diff --git a/modules/nf-core/cellranger/count/tests/tags.yml b/modules/nf-core/cellranger/count/tests/tags.yml
diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -22,7 +22,7 @@ workflow SCRNASEQ {
 
     main:
 
-    protocol_config = WorkflowScrnaseq.getProtocol(workflow, log, params.aligner, params.protocol)
+    protocol_config = Utils.getProtocol(workflow, log, params.aligner, params.protocol)
     if (protocol_config['protocol'] == 'auto' && params.aligner != "cellranger") {
         error "Only cellranger supports `protocol = 'auto'`. Please specify the protocol manually!"
     }