Skip to content

SmartSeq - Bugfixes #486

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

Open
wants to merge 9 commits into
base: dev
Choose a base branch
from
Open

SmartSeq - Bugfixes #486

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
313e813
Account for the case where no whitelist was provided
sminot Jul 29, 2025
409b14a
If the SmartSeq protocol is used, set soloUMIdedup to NoDedup
sminot Jul 29, 2025
8c74140
Skip seurat object when only 1 cell is detected
sminot Jul 29, 2025
4034422
Must escape in a template
sminot Jul 29, 2025
7f9c592
rds is optional
sminot Jul 30, 2025
b0ba2e5
Fix unbound variable
sminot Jul 31, 2025
65feb08
Filtered counts are not always present
sminot Aug 1, 2025
9160800
Merge branch 'dev' into fix_no_whitelist
nictru Aug 2, 2025
8a668e3
Merge branch 'dev' into fix_no_whitelist
sminot Aug 4, 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 modules/local/anndatar_convert.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ process ANNDATAR_CONVERT {
tuple val(meta), path(h5ad)

output:
tuple val(meta), path("${meta.id}_${meta.input_type}_matrix*.rds"), emit: rds
tuple val(meta), path("${meta.id}_${meta.input_type}_matrix*.rds"), emit: rds, optional: true
path "versions.yml" , emit: versions

when:
Expand Down
27 changes: 22 additions & 5 deletions modules/local/star_align.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ process STAR_ALIGN {
tuple val(meta), path('*d.out.bam') , emit: bam
tuple val(meta), path('*.Solo.out') , emit: counts
tuple val(meta), path ("*.Solo.out/Gene*/raw") , emit: raw_counts
tuple val(meta), path ("*.Solo.out/Gene*/filtered") , emit: filtered_counts
tuple val(meta), path ("*.Solo.out/Gene*/filtered") , emit: filtered_counts, optional: true
tuple val(meta), path ("*.Solo.out/Velocyto/velocyto_raw") , emit: raw_velocyto, optional:true
tuple val(meta), path ("*.Solo.out/Velocyto/velocyto_filtered"), emit: filtered_velocyto, optional:true
tuple val(meta), path('*Log.final.out') , emit: log_final
Expand Down Expand Up @@ -61,20 +61,37 @@ process STAR_ALIGN {
// separate forward from reverse pairs
def (forward, reverse) = reads.collate(2).transpose()
"""
if [[ $whitelist == *.gz ]]; then
gzip -cdf $whitelist > whitelist.uncompressed.txt
# If the whitelist was not provided
if [[ -z "$whitelist" ]]; then
echo "Whitelist file not provided." >&2
soloCBwhitelistArg=""
else
cp $whitelist whitelist.uncompressed.txt
if [[ "$whitelist" == *.gz ]]; then
gzip -cdf "$whitelist" > whitelist.uncompressed.txt
else
cp "$whitelist" whitelist.uncompressed.txt
fi
soloCBwhitelistArg="--soloCBwhitelist whitelist.uncompressed.txt"
echo "Whitelist file provided - $whitelist." >&2
fi

# If the SmartSeq protocol is used, set soloUMIdedup to NoDedup
if [[ "$protocol" == "SmartSeq" ]]; then
echo "SmartSeq protocol detected, setting --soloUMIdedup to NoDedup." >&2
soloUMIdedupArg="--soloUMIdedup NoDedup"
Comment on lines +79 to +81
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

But hopefully the modifications are still useful even if users provide the appropriate parameters for SmartSeq3 data as well?

I was specifically refering to this statement. For SmartSeq3 UMI deduplication should be enabled.

Copy link
Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

My apologies, I should have realized that. I agree that the UMI deduplication should be able to enabled by the user. I will leave it to you whether that should be done by setting the protocol param (differentiating SmartSeq2 and SmartSeq3), or simply letting the UMI deduplication be a separate parameter. I can implement if you advise on your preferred approach.

else
soloUMIdedupArg=""
fi

STAR \\
--genomeDir $index \\
--readFilesIn ${reverse.join( "," )} ${forward.join( "," )} \\
--runThreadN $task.cpus \\
--outFileNamePrefix $prefix. \\
--soloCBwhitelist whitelist.uncompressed.txt \\
\$soloCBwhitelistArg \\
--soloType $protocol \\
--soloFeatures $star_feature \\
\$soloUMIdedupArg \\
$other_10x_parameters \\
$out_sam_type \\
$ignore_gtf \\
Expand Down
35 changes: 21 additions & 14 deletions modules/local/templates/anndatar_convert.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,20 +9,27 @@ library(SingleCellExperiment)

# read input
adata <- read_h5ad("${h5ad}")

# convert to Seurat
obj <- adata\$to_Seurat()

# save files
dir.create(file.path("$meta.id"), showWarnings = FALSE)
saveRDS(obj, file = "${meta.id}_${meta.input_type}_matrix.seurat.rds")

# convert to SingleCellExperiment
obj <- adata\$to_SingleCellExperiment()

# save files
dir.create(file.path("$meta.id"), showWarnings = FALSE)
saveRDS(obj, file = "${meta.id}_${meta.input_type}_matrix.sce.rds")
print("Read in ${h5ad} successfully.")
print(adata)

# If there is only 1 cell
if(adata\$shape()[1] == 1) {
print("The input file contains only one cell. Cannot create Seurat object.")
}else{
# convert to Seurat
obj <- adata\$to_Seurat()

# save files
dir.create(file.path("$meta.id"), showWarnings = FALSE)
saveRDS(obj, file = "${meta.id}_${meta.input_type}_matrix.seurat.rds")

# convert to SingleCellExperiment
obj <- adata\$to_SingleCellExperiment()

# save files
dir.create(file.path("$meta.id"), showWarnings = FALSE)
saveRDS(obj, file = "${meta.id}_${meta.input_type}_matrix.sce.rds")
}

#
# save versions file
Expand Down