Merge pull request #348 from nick-youngblut/cellranger_10XV4

Cellranger 10XV4

CHANGELOG.md

@@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+- Add support for 10XV4 chemistry ([#348](https://github.com/nf-core/scrnaseq/pull/348))
+
 ## v2.7.0 - 2024-06-03
 
 - Apply `check_max` to AlevinQC time limit ([#335](https://github.com/nf-core/scrnaseq/pull/335))

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.
 

nextflow_schema.json

@@ -65,8 +65,8 @@
                 },
                 "protocol": {
                     "type": "string",
-                    "description": "The protocol that was used to generate the single cell data, e.g. 10x Genomics v2 Chemistry.\n\n Can be 'auto' (cellranger only), '10XV1', '10XV2', '10XV3', or any other protocol string that will get directly passed the respective aligner.",
-                    "help_text": "The default is to auto-detect the protocol when running cellranger. For all other aligners the protocol MUST be manually specified. \n\n The following protocols are recognized by the pipeline and mapped to the corresponding protocol name of the respective aligner: '10XV1', '10XV2', '10XV3'. \n\nAny other protocol value is passed to the aligner in verbatim to support other sequencing platforms. See the [kallisto](https://pachterlab.github.io/kallisto/manual#bus), [simpleaf](https://simpleaf.readthedocs.io/en/latest/quant-command.html#a-note-on-the-chemistry-flag), [starsolo](https://gensoft.pasteur.fr/docs/STAR/2.7.9a/STARsolo.html), and [universc](https://github.com/minoda-lab/universc#pre-set-configurations) documentations for more details.",
+                    "description": "The protocol that was used to generate the single cell data, e.g. 10x Genomics v2 Chemistry.\n\n Can be 'auto' (cellranger only), '10XV1', '10XV2', '10XV3', '10XV4', or any other protocol string that will get directly passed the respective aligner.",
+                    "help_text": "The default is to auto-detect the protocol when running cellranger. For all other aligners the protocol MUST be manually specified. \n\n The following protocols are recognized by the pipeline and mapped to the corresponding protocol name of the respective aligner: '10XV1', '10XV2', '10XV3', '10XV4'. \n\nAny other protocol value is passed to the aligner in verbatim to support other sequencing platforms. See the [kallisto](https://pachterlab.github.io/kallisto/manual#bus), [simpleaf](https://simpleaf.readthedocs.io/en/latest/quant-command.html#a-note-on-the-chemistry-flag), [starsolo](https://gensoft.pasteur.fr/docs/STAR/2.7.9a/STARsolo.html), and [universc](https://github.com/minoda-lab/universc#pre-set-configurations) documentations for more details.",
                     "default": "auto",
                     "fa_icon": "fas fa-cogs"
                 }