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Added new parameter cellbender_extraargs for CellBender #59

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Merged
bonitavw merged 1 commit into from
Mar 4, 2026
Merged

Added new parameter cellbender_extraargs for CellBender #59

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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -9,3 +9,4 @@ logs/*
seperate_scripts/*
conf/[0-9]*
work/*
*scale*
3 changes: 2 additions & 1 deletion modules/local/tools/cellbender/main.nf
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Expand Up @@ -32,6 +32,7 @@ process CELLBENDER {
--output cellbender_output.h5 \\
--epochs 150 \\
--expected-cells ${meta.expected_cells} \\
--fpr 0.01
--fpr 0.01 \\
${params.cellbender_extraargs ?: ''}
"""
}
1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -73,6 +73,7 @@ params {

// Filtering parameters
perform_cellbender = false
cellbender_extraargs = null

// Parameters for external pipelines
splitpipe_installation = null
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