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Wilms 06 module: Update and re-render 04 notebook #867

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merged 4 commits into from
Nov 7, 2024
Merged

Wilms 06 module: Update and re-render 04 notebook #867

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d1f0a88
add some words to dictionary
sjspielman Nov 7, 2024
db338fa
Fix typos and sample_id loop bug, and the file was also styled
sjspielman Nov 7, 2024
68917a3
re-render notebooks
sjspielman Nov 7, 2024
92c886e
Add remaining workflow steps to script, only some of which is current…
sjspielman Nov 7, 2024
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3 changes: 3 additions & 0 deletions .github/components/dictionary.txt
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,8 @@ doxxing
dropdown
ECM
ECR
endothelia
endothelial
endothelium
enforceability
Ensembl
Expand Down Expand Up @@ -191,6 +193,7 @@ scRNA
scrublet
SEACells
SemVar
seq
SingleR
snRNA
socio
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58 changes: 49 additions & 9 deletions analyses/cell-type-wilms-tumor-06/00_run_workflow.sh
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Expand Up @@ -110,20 +110,60 @@ for sample_dir in ${data_dir}/${project_id}/SCPCS*; do
fi
done

# Temporarily this code is not run in CI.
if [[ $IS_CI -eq 0 ]]; then

# Run notebook template to explore label transfer and clustering for all samples at once
Rscript -e "rmarkdown::render('${notebook_output_dir}/04_annotation_Across_Samples_exploration.Rmd',
output_format = 'html_document',
output_file = '04_annotation_Across_Samples_exploration.html',
output_dir = ${notebook_output_dir})"
# This step is run here because it must be run both for:
# - scripts/explore-cnv-methods.R (exploratory; calls 06_infercnv.R)
# - 06_infercnv.R (not exploratory)
Rscript scripts/06a_build-geneposition.R

# These steps do not directly contribute to the final annotations
if [[ $RUN_EXPLORATORY -eq 1 ]]; then

# Build the gene position file reference for infercnv
Rscript scripts/06a_build-geneposition.R
# Run notebook template to explore label transfer and clustering for all samples at once
for score_threshold in 0.5 0.75 0.85 0.95; do
Rscript -e "rmarkdown::render('${notebook_output_dir}/04_annotation_Across_Samples_exploration.Rmd',
params = list(predicted.score_thr = ${score_threshold}),
output_format = 'html_document',
output_file = '04_annotation_Across_Samples_exploration_predicted.score_threshold_${score_threshold}.html',
output_dir = '${notebook_output_dir}')"
done

# Run infercnv and copykat for a selection of samples
# This script calls scripts/05_copyKAT.R and scripts/06_infercnv.R
Rscript scripts/explore-cnv-methods.R

fi


# Temporarily, this code is not run in CI
if [[ $IS_CI -eq 0 ]]; then

# Run infercnv for all samples with HMM i3 and using "both" as the reference
for sample_dir in ${data_dir}/${project_id}/SCPCS*; do
sample_id=$(basename $sample_dir)

# These samples do not have sufficient normal cells to run with a reference in infercnv
samples_no_reference=("SCPCS000177" "SCPCS000180" "SCPCS000181" "SCPCS000190" "SCPCS000197")

# Define inferCNV reference set
if [[ " ${samples_no_reference[*]} " =~ " ${sample_id} " ]]; then
reference="none"
else
reference="both"
fi

# don't repeat inference on selection of samples since certain
# output files will already exist if exploratory steps were run
output_file="${results_dir}/${sample_id}/06_infercnv_HMM-i3_${sample_id}_reference-${reference}.rds"
if [[ ! -f $output_file ]]; then
Rscript scripts/06_infercnv.R --sample_id $sample_id --reference $reference --HMM i3
fi
done

# Render notebook to make draft annotations
Rscript -e "rmarkdown::render('${notebook_template_dir}/07_combined_annotation_across_samples_exploration.Rmd',
params = list(predicted.celltype.threshold = 0.85, cnv_threshold = 0),
output_format = 'html_document',
output_file = '07_combined_annotation_across_samples_exploration.html',
output_dir = '${notebook_template_dir}')"
fi
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