Skip to content

Add support for Cellranger 10 #20

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
skchronicles merged 7 commits into from
Dec 18, 2025
Merged

Add support for Cellranger 10 #20

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
4d61b17
Adding support for Cell Ranger 10
chenv3 Dec 17, 2025
f8f1a3d
Fix: during final check only store type information if present in file
chenv3 Dec 17, 2025
23cfb06
Fix: changing the order where silhouette output files are saved and h…
chenv3 Dec 17, 2025
020b5f8
Fix: edit generateSummaryFiles_MULTI.py so that values less than or e…
chenv3 Dec 17, 2025
113cdbb
Bump version
chenv3 Dec 18, 2025
b476bdc
Bump version
chenv3 Dec 18, 2025
df4d476
Merge branch 'main' into cellranger10
chenv3 Dec 18, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion VERSION
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
3.1.0
3.2.0
6 changes: 3 additions & 3 deletions cell-seek
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -517,11 +517,11 @@ def parsed_arguments(name, description):
options: hg38, mm10, hg2024, mm2024.
Example: --genome hg38
{3}{4}Analysis options:{5}
--cellranger {{7.1.0, 7.2.0, 8.0.0, 9.0.0}}
--cellranger {{7.1.0, 7.2.0, 8.0.0, 9.0.0, 10.0.0}}
The version of CellRanger to run. This option specifies
which version of CellRanger to use when running GEX,
CITE, or MULTI. Please select one of the following
options: 7.1.0, 7.2.0, 8.0.0, 9.0.0
options: 7.1.0, 7.2.0, 8.0.0, 9.0.0, 10.0.0
Example: --cellranger 7.1.0
--aggregate {{mapped,none}}
Cell Ranger aggregate. This option defines the
Expand Down Expand Up @@ -1047,7 +1047,7 @@ def parsed_arguments(name, description):
type=str.lower,
required=False,
default="",
choices=["7.1.0", "7.2.0", "8.0.0", "9.0.0"],
choices=["7.1.0", "7.2.0", "8.0.0", "9.0.0", "10.0.0"],
help=argparse.SUPPRESS,
)

Expand Down
2 changes: 1 addition & 1 deletion config/modules.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"tools": {
"cellranger": {"7.1.0": "cellranger/7.1.0", "7.2.0": "cellranger/7.2.0", "8.0.0": "cellranger/8.0.0", "9.0.0": "cellranger/9.0.0"},
"cellranger": {"7.1.0": "cellranger/7.1.0", "7.2.0": "cellranger/7.2.0", "8.0.0": "cellranger/8.0.0", "9.0.0": "cellranger/9.0.0", "10.0.0": "cellranger/10.0.0"},
"cellranger-atac": "cellranger-atac/2.1.0",
"cellranger-arc": "cellranger-arc/2.0.1",
"python2": "python/2.7",
Expand Down
16 changes: 8 additions & 8 deletions docs/usage/run.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -84,11 +84,11 @@ Each of the following arguments are required. Failure to provide a required argu
> ***Example:*** `--genome hg2024`

---
`--cellranger {7.1.0, 7.2.0, 8.0.0, 9.0.0}`
`--cellranger {7.1.0, 7.2.0, 8.0.0, 9.0.0, 10.0.0}`
> **The version of Cell Ranger to run.**
> *type: string*
>
> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0, 9.0.0
> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0, 9.0.0, 10.0.0
>
> ***Example:*** `--cellranger 7.1.0`

Expand Down Expand Up @@ -269,11 +269,11 @@ Each of the following arguments are required. Failure to provide a required argu
> ***Example:*** `--genome hg38`

---
`--cellranger {7.1.0, 7.2.0, 8.0.0, 9.0.0}`
`--cellranger {7.1.0, 7.2.0, 8.0.0, 9.0.0, 10.0.0}`
> **The version of Cell Ranger to run.**
> *type: string*
>
> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0, 9.0.0
> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0, 9.0.0, 10.0.0
>
> ***Example:*** `--cellranger 7.1.0`

Expand Down Expand Up @@ -355,11 +355,11 @@ Each of the following arguments are required. Failure to provide a required argu
> ***Example:*** `--genome hg38`

---
`--cellranger {7.1.0, 7.2.0, 8.0.0, 9.0.0}`
`--cellranger {7.1.0, 7.2.0, 8.0.0, 9.0.0, 10.0.0}`
> **The version of Cell Ranger to run.**
> *type: string*
>
> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0, 9.0.0
> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0, 9.0.0, 10.0.0
>
> ***Example:*** `--cellranger 7.1.0`

Expand Down Expand Up @@ -523,11 +523,11 @@ Each of the following arguments are required. Failure to provide a required argu
> ***Example:*** `--genome hg38`

---
`--cellranger {7.1.0, 7.2.0, 8.0.0, 9.0.0}`
`--cellranger {7.1.0, 7.2.0, 8.0.0, 9.0.0, 10.0.0}`
> **The version of Cell Ranger to run.**
> *type: string*
>
> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0, 9.0.0
> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0, 9.0.0, 10.0.0
>
> ***Example:*** `--cellranger 7.1.0`

Expand Down
7 changes: 4 additions & 3 deletions src/run.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -828,9 +828,10 @@ def finalcheck(config, flag, delimeter=','):
values = contents.get(i, set())
values.add(linelist[indices[i]])
contents[i] = values
value = name_type.get(linelist[indices['name']], set())
value.add(linelist[indices['type']])
name_type[linelist[indices['name']]] = value
if 'type' in indices:
value = name_type.get(linelist[indices['name']], set())
value.add(linelist[indices['type']])
name_type[linelist[indices['name']]] = value

# Compiles the sample names and fastq paths from the input (config)
samples = set([re.sub("_S[0-9]+_L00[0-9]", "", i) for i in config['samples']])
Expand Down
5 changes: 4 additions & 1 deletion workflow/scripts/generateSummaryFiles_MULTI.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,10 @@ def write_sheet(workbook, stats, samples, headers, filter):
if i.count('.') > 1:
worksheet.write(row, col, i.replace(',', ''))
else:
worksheet.write(row, col, float(i.replace(',','')), formatFrac)
if float(i.replace(',','')) <= 1:
worksheet.write(row, col, float(i.replace(',','')), formatPer)
else:
worksheet.write(row, col, float(i.replace(',','')), formatFrac)
elif len(re.findall('\D', ''.join(re.findall('[^,]', i)))) > 0:
worksheet.write(row, col, i)
else:
Expand Down
2 changes: 1 addition & 1 deletion workflow/scripts/seuratSampleQC.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -226,11 +226,11 @@ for(resolution in c(0.1, seq(0.2,1.0,0.2), 1.5, 2.0)){
try({
clusters <- Idents(seur)
sil<-silhouette(as.numeric(clusters), dist=d)
write.csv(sil, paste0('SilhouetteResult_res.', resolution, '.csv'), row.names=F, quote=F)
pdf(paste0("SilhouettePlot_res.",resolution,".pdf"))
print(plot(sil, col=as.factor(clusters[order(clusters, decreasing=FALSE)]), main=paste("Silhouette plot of Seurat clustering - resolution ", resolution, sep=""), lty=2))
print(abline(v=mean(sil[,3]), col="red4", lty=2))
dev.off()
write.csv(sil, paste0('SilhouetteResult_res.', resolution, '.csv'), row.names=F, quote=F)
})
}

Expand Down
2 changes: 1 addition & 1 deletion workflow/scripts/seuratSampleQCReport.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -161,7 +161,7 @@ sil_files <- Sys.glob(file.path(seuratdir, "SilhouetteResult_res*.csv"))
resolutions <- sapply(files, function(x) (x %>% basename %>% tools::file_path_sans_ext() %>% strsplit(split='res.'))[[1]][2]) %>% str_sort(numeric=T)
sil_mean <- sapply(resolutions, function(resolution) {filename <- grep(paste0('res.', resolution, '.csv'), sil_files, value=T); if(length(filename) > 0) { data <- read.csv(filename); mean(data$sil_width)} else{-Inf}})

if (max(sil_mean) > -Inf) {
if (max(sil_mean, na.rm=T) > -Inf) {
cat("The average silhouette score and a silhouette plot was calculated for each cluster resolution. This was done by calculating the score for each cell using the euclidean distance generated based on the cell's principal components to obtain an independent measure of the clustering results. The silhouette score ranges from -1 to 1, where: \n\n* 1 means that clusters are far apart and data points close to each other are assigned the same cluster label\n\n* 0 means that the distance between clusters are not signifcant and data points are close to more than one cluster\n\n* -1 means that clusters may be incorrectly assigned and data points are closer to other clusters than other data points in its own cluster\n\nThe resolution with the highest detected average silhouette score is resolution", sil_mean %>% which.max %>% names, "\n\n")
}

Expand Down