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Add scds module #6907

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7 changes: 7 additions & 0 deletions modules/nf-core/scds/environment.yml
Original file line number Diff line number Diff line change
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channels:
- conda-forge
- bioconda
dependencies:
- bioconda::bioconductor-scds=1.18.0
- conda-forge::r-seurat=5.1.0
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- conda-forge::r-xgboost=1.7.6
36 changes: 36 additions & 0 deletions modules/nf-core/scds/main.nf
Original file line number Diff line number Diff line change
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process SCDS {
tag "$meta.id"
label 'process_medium'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioconductor-scds:1.18.0--r43hdfd78af_0':
'biocontainers/bioconductor-scds:1.18.0--r43hdfd78af_0' }"

input:
tuple val(meta), path(rds)

output:
tuple val(meta), path("*.rds"), emit: rds
tuple val(meta), path("*.csv"), emit: predictions
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when

script:
prefix = task.ext.prefix ?: "${meta.id}"
template 'scds.R'

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.rds
touch ${prefix}.csv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scds: \$(Rscript -e "library(scds); cat(as.character(packageVersion('scds')))")
END_VERSIONS
"""
}
59 changes: 59 additions & 0 deletions modules/nf-core/scds/meta.yml
Original file line number Diff line number Diff line change
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---
name: scds
description: Module to use scds for doublet scoring
keywords:
- doublet
- single-cell
- transcriptomics
tools:
- scds:
description: scds is an in-silico doublet annotation tool for single cell RNA sequencing data
homepage: https://www.bioconductor.org/packages/release/bioc/html/scds.html
documentation: https://www.bioconductor.org/packages/release/bioc/vignettes/scds/inst/doc/scds.html
tool_dev_url: https://github.com/kostkalab/scds
doi: 10.1093/bioinformatics/btz698
licence: ["MIT"]
identifier: biotools:scds

input:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
- rds:
type: file
description: RDS file containing filtered data (without empty droplets) in SingleCellExperiment format
pattern: "*.rds"

output:
- rds:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- "*.rds":
type: file
description: RDS file containing doublet scores in SingleCellExperiment format
pattern: "*.rds"
- predictions:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- "*.csv":
type: file
description: CSV file containing doublet scores
pattern: "*.csv"
- versions:
- versions.yml:
type: file
description: File containing software version
pattern: "versions.yml"

authors:
- "@cakirb"
maintainers:
- "@cakirb"
52 changes: 52 additions & 0 deletions modules/nf-core/scds/templates/scds.R
Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
#!/usr/bin/env Rscript

library(scds)
library(SingleCellExperiment)

sce <- readRDS("${rds}")

sce <- Seurat::as.SingleCellExperiment(sce)

## Annotate doublet using binary classification based doublet scoring:
sce <- bcds(sce, retRes = TRUE, estNdbl=TRUE)

## Annotate doublet using co-expression based doublet scoring:
try({
sce <- cxds(sce, retRes = TRUE, estNdbl=TRUE)
})

### If cxds worked, run hybrid, otherwise use bcds annotations
if ("cxds_score" %in% colnames(colData(sce))) {
## Combine both annotations into a hybrid annotation
sce <- cxds_bcds_hybrid(sce, estNdbl=TRUE)

predictions <- colData(sce)[, 'hybrid_call', drop=FALSE]
} else {
predictions <- colData(sce)[, 'bcds_call', drop=FALSE]
}

saveRDS(sce, "${prefix}.rds")

colnames(predictions) <- "${prefix}"
write.csv(predictions, "${prefix}.csv")

################################################
################################################
## VERSIONS FILE ##
################################################
################################################

r.version <- strsplit(version[['version.string']], ' ')[[1]][3]
scds.version <- as.character(packageVersion('scds'))

writeLines(
c(
'"${task.process}":',
paste(' scds:', scds.version)
),
'versions.yml')

################################################
################################################
################################################
################################################
52 changes: 52 additions & 0 deletions modules/nf-core/scds/tests/main.nf.test
Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
nextflow_process {
name 'Test Process SCDS'
script '../main.nf'
process 'SCDS'

tag "modules"
tag "modules_nfcore"
tag "scds"

test("test_scds") {
when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix.rds", checkIfExists: true) ]
"""
}
}
then {
assertAll(
{assert process.success},
{assert snapshot(process.out.rds).match("res_scds_rds")},
{assert snapshot(process.out.csv).match("res_scds_csv")},
{assert snapshot(process.out.versions).match("res_scds_versions")}
)
}
}

test("test_scds - stub") {
options '-stub'

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix.rds", checkIfExists: true) ]
]
"""
}
}
then {
assertAll(
{assert process.success},
{assert snapshot(process.out.rds).match("res_scds_rds_stub")},
{assert snapshot(process.out.csv).match("res_scds_csv_stub")},
{assert snapshot(process.out.versions).match("res_scds_versions_stub")}
)
}
}
}
34 changes: 34 additions & 0 deletions modules/nf-core/scds/tests/main.nf.test.snap
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
{
"res_scds_csv": {
"content": null,
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.04.4"
},
"timestamp": "2024-10-29T11:50:55.821158"
},
"res_scds_versions": {
"content": [
[

]
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.04.4"
},
"timestamp": "2024-10-29T11:50:55.827718"
},
"res_scds_rds": {
"content": [
[

]
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.04.4"
},
"timestamp": "2024-10-29T11:50:55.808717"
}
}
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