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Add perform_celltyping parameter #506

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merged 6 commits into from
Oct 16, 2023
Merged

Add perform_celltyping parameter #506

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d4a78c9
parameter for performing cell typing
allyhawkins Oct 12, 2023
6ada409
make cell type report optional
allyhawkins Oct 13, 2023
e8afcbe
Merge branch 'allyhawkins/celltypes-to-sce' into allyhawkins/perform-…
allyhawkins Oct 13, 2023
d167b77
Apply suggestions from code review
allyhawkins Oct 13, 2023
a47b1d7
Merge branch 'development' into allyhawkins/perform-celltyping
allyhawkins Oct 13, 2023
01dc6cf
use results='asis'
allyhawkins Oct 16, 2023
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12 changes: 8 additions & 4 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -224,12 +224,16 @@ workflow {
// Cluster SCE
cluster_sce(post_process_sce.out)

// Perform celltyping, if specified
annotate_celltypes(cluster_sce.out)

if(params.perform_celltyping){
// Perform celltyping, if specified
annotated_celltype_ch = annotate_celltypes(cluster_sce.out)
} else {
annotated_celltype_ch = cluster_sce.out
}

// generate QC reports
sce_qc_report(
annotate_celltypes.out,
annotated_celltype_ch,
report_template_tuple
)

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19 changes: 11 additions & 8 deletions modules/qc-report.nf
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Expand Up @@ -19,15 +19,17 @@ process sce_qc_report{
metadata_json = "${meta.library_id}_metadata.json"
workflow_url = workflow.repository ?: workflow.manifest.homePage
workflow_version = workflow.revision ?: workflow.manifest.version

// names for final output files
unfiltered_out = "${meta.library_id}_unfiltered.rds"
filtered_out = "${meta.library_id}_filtered.rds"
processed_out = "${meta.library_id}_processed.rds"

// check for cell types
// TODO: add `params.perform_celltyping && (...)` when implemented
has_celltypes = (meta.submitter_cell_types_file || meta.singler_model_file || meta.cellassign_reference_file)
// only provide report template if cell typing was performed and either singler or cellassign was used
has_celltypes = (params.perform_celltyping
&& (meta.singler_model_file || meta.cellassign_reference_file)
)
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celltype_report = "${meta.library_id}_celltype-report.html" // rendered HTML
celltype_template_path = "${template_dir}/${celltype_template_file}" // template input

Expand Down Expand Up @@ -69,9 +71,10 @@ process sce_qc_report{
processed_out = "${meta.library_id}_processed.rds"
qc_report = "${meta.library_id}_qc.html"
metadata_json = "${meta.library_id}_metadata.json"

// TODO: add `params.perform_celltyping && (...)` when implemented
has_celltypes = meta.submitter_cell_types_file || meta.singler_model_file || meta.cellassign_reference_file

has_celltypes = (params.perform_celltyping
&& (meta.singler_model_file || meta.cellassign_reference_file)
)
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celltype_report = "${meta.library_id}_celltype-report.html" // rendered HTML

"""
Expand All @@ -80,7 +83,7 @@ process sce_qc_report{
touch ${processed_out}
touch ${qc_report}
${has_celltypes ? "touch ${celltype_report}" : ""}

echo '{"unfiltered_cells": 10, "filtered_cells": 10, "processed_cells": 10}' > ${metadata_json}
"""
}
3 changes: 2 additions & 1 deletion nextflow.config
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Expand Up @@ -38,6 +38,7 @@ params {
skip_genetic_demux = false // skip genetic demultiplexing steps, even if bulk data is present
publish_fry_outs = false // alevin-fry outputs are not published by default. Use `--publish_fry_outs` to publish these files to the `checkpoints` folder.
spliced_only = false // include only spliced reads in counts matrix, by default both unspliced and spliced reads are totaled and found in `counts` asasy of returned SingleCellExperiment object
perform_celltyping = false // specify whether or not to incorporate cell type annotations

seed = 2021 // random number seed for filtering and post-processing (0 means use system seed)

Expand All @@ -54,7 +55,7 @@ params {

// Cell type annotation options
singler_label_name = "label.ont" // celldex reference label used for SingleR reference building

// Docker container images
includeConfig 'config/containers.config'

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10 changes: 9 additions & 1 deletion templates/qc_report/celltypes_qc.rmd
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Expand Up @@ -171,7 +171,15 @@ knitr::asis_output(
)
```

For additional information about cell typing, including diagnostic plots and/or heatmap comparisons among annotations (if available), please refer to the [supplementary cell type QC report](`r params$celltype_report`).

<!-- At least one cell type annotation method required for the supplemental report -->
```{r, eval = has_singler | has_cellassign}
knitr::asis_output(
glue::glue("
For additional information about cell typing, including diagnostic plots and/or heatmap comparisons among annotations (if available), please refer to the [supplementary cell type QC report](`r params$celltype_report`).
")
)
```
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Is there a reason we are wrapping here and above rather than using the chunk options? I think knitr::asis_output() is useful if we have a mix of outputs, but kind of distracting if the entire chunk is asis

Suggested change
```{r, eval = has_singler | has_cellassign}
knitr::asis_output(
glue::glue("
For additional information about cell typing, including diagnostic plots and/or heatmap comparisons among annotations (if available), please refer to the [supplementary cell type QC report](`r params$celltype_report`).
")
)
```
````{r, eval = has_singler | has_cellassign, result = 'asis'}
glue::glue("
For additional information about cell typing, including diagnostic plots and/or heatmap comparisons among annotations (if available), please refer to the [supplementary cell type QC report](`r params$celltype_report`).
")

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Honestly, the only reason I did it this way was to mirror how the other sections were. But we can change to using result='asis' throughout instead of knitr::asis_output?



## Statistics
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2 changes: 1 addition & 1 deletion templates/qc_report/main_qc_report.rmd
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Expand Up @@ -124,7 +124,7 @@ if (has_processed) {
}

# check for celltypes_report if celltypes are present
if (has_celltypes & is.null(params$celltype_report)) {
if ((has_singler | has_cellassign) & is.null(params$celltype_report)) {
stop("Cell type annotations were provided but the parameter specifying the cell type report file is missing.")
}
```
Expand Down