Release v2.7.1

.nf-core.yml

@@ -6,6 +6,3 @@ lint:
     - .github/ISSUE_TEMPLATE/bug_report.yml
   files_exist:
     - lib/Utils.groovy
-  # TODO This is because of an issue with the monochromeLogs parameter
-  # See nextflow.config for details
-  schema_params: False

CHANGELOG.md

@@ -3,6 +3,14 @@
 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).
 
+## v2.7.1 - 2024-08-13
+
+- Re-enable linting check for nextflow schema ([#354](https://github.com/nf-core/scrnaseq/pull/354))
+- Add support for 10XV4 chemistry ([#348](https://github.com/nf-core/scrnaseq/pull/348))
+- Fix issues with predefined STAR index ([#350](https://github.com/nf-core/scrnaseq/pull/350))
+- Update modules ([#351](https://github.com/nf-core/scrnaseq/pull/351))
+- Fix resource specifications for `cellranger mkref`/`cellrangerarc mkref` ([#352](https://github.com/nf-core/scrnaseq/pull/352))
+
 ## v2.7.0 - 2024-06-03
 
 - Apply `check_max` to AlevinQC time limit ([#335](https://github.com/nf-core/scrnaseq/pull/335))

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/releases/tag/2.7.0" target="_blank">nf-core/scrnaseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/releases/tag/2.7.1" 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/2.7.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/scrnaseq/2.7.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-scrnaseq-methods-description":
     order: -1000

assets/protocols.json

@@ -12,6 +12,10 @@
             "protocol": "10xv3",
             "whitelist": "assets/whitelist/10x_V3_barcode_whitelist.txt.gz"
         },
+        "10XV4": {
+            "protocol": "10xv4",
+            "whitelist": "assets/whitelist/10x_V4_barcode_whitelist.txt.gz"
+        },
         "dropseq": {
             "protocol": "dropseq"
         }
@@ -28,6 +32,9 @@
         },
         "10XV3": {
             "protocol": "SC3Pv3"
+        },
+        "10XV4": {
+            "protocol": "SC3Pv4"
         }
     },
     "cellrangerarc": {
@@ -51,6 +58,11 @@
             "extra_args": "--soloUMIlen 12",
             "whitelist": "assets/whitelist/10x_V3_barcode_whitelist.txt.gz"
         },
+        "10XV4": {
+            "protocol": "CB_UMI_Simple",
+            "extra_args": "--soloUMIlen 12",
+            "whitelist": "assets/whitelist/10x_V4_barcode_whitelist.txt.gz"
+        },
         "dropseq": {
             "protocol": "CB_UMI_Simple"
         },
@@ -68,6 +80,9 @@
         "10XV3": {
             "protocol": "10XV3"
         },
+        "10XV4": {
+            "protocol": "10XV4"
+        },
         "dropseq": {
             "protocol": "DROPSEQ"
         },
@@ -88,6 +103,9 @@
         "10XV3": {
             "protocol": "10x-v3"
         },
+        "10XV4": {
+            "protocol": "10x-v4"
+        },
         "dropseq": {
             "protocol": "dropseq"
         }

docs/usage.md

@@ -85,7 +85,7 @@ The single-cell protocol used in the experiment can be specified using the `--pr
 For cellranger, it is recommended to stick with the default value `'auto'` for automatic detection of the protocol.
 For all other aligner, you need to specify the protocol manually.
 
-The three 10x Genomics protocols 3' v1 (`10XV1`), 3' v2 (`10XV2`) and 3' v3 (`10XV3`) are universally supported
+The three 10x Genomics protocols 3' v1 (`10XV1`), 3' v2 (`10XV2`), 3' v3 (`10XV3`), and 3' v4 (`10XV4`) are universally supported
 by all aligners in the pipeline and mapped to the correct options automatically. If the protocol is unknown to the
 nf-core pipeline, the value specified to `--protocol` is passed to the aligner _in verbatim_ to support additional protocols.
 

modules.json

@@ -7,17 +7,17 @@
                 "nf-core": {
                     "cellranger/count": {
                         "branch": "master",
-                        "git_sha": "e66183d2ab6a5c2f3fd66b2bee942287cf65536c",
+                        "git_sha": "90dad5491658049282ceb287a3d7732c1ce39837",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkgtf": {
                         "branch": "master",
-                        "git_sha": "e66183d2ab6a5c2f3fd66b2bee942287cf65536c",
+                        "git_sha": "90dad5491658049282ceb287a3d7732c1ce39837",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkref": {
                         "branch": "master",
-                        "git_sha": "e66183d2ab6a5c2f3fd66b2bee942287cf65536c",
+                        "git_sha": "3549a361ce3401b6afd238a266389d78392a53f6",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkvdjref": {
@@ -27,7 +27,7 @@
                     },
                     "cellranger/multi": {
                         "branch": "master",
-                        "git_sha": "5f12fc2128f419a8750c5b0620e4b54d7aa33fec",
+                        "git_sha": "90dad5491658049282ceb287a3d7732c1ce39837",
                         "installed_by": ["modules"]
                     },
                     "cellrangerarc/count": {
@@ -42,12 +42,12 @@
                     },
                     "cellrangerarc/mkref": {
                         "branch": "master",
-                        "git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
+                        "git_sha": "3549a361ce3401b6afd238a266389d78392a53f6",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "gffread": {
@@ -57,7 +57,7 @@
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     },
                     "kallistobustools/count": {
@@ -72,12 +72,12 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "universc": {
@@ -87,7 +87,7 @@
                     },
                     "unzip": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "b0c3ff2485534c09d9debbf20125d9c6b72ce118",
                         "installed_by": ["modules"]
                     }
                 }