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Make Bleeding Correction Optional in Visium10x Pipeline #133

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Dec 21, 2023
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Make Bleeding Correction Optional in Visium10x Pipeline #133

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1 change: 1 addition & 0 deletions docs/.gitignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
_build/
18 changes: 13 additions & 5 deletions nextflow/subworkflows/bayestme/bayestme_basic_visium_analysis/main.nf
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Expand Up @@ -24,11 +24,19 @@ workflow BAYESTME_BASIC_VISIUM_ANALYSIS {

BAYESTME_FILTER_GENES( filter_genes_input )

BAYESTME_BLEEDING_CORRECTION( BAYESTME_FILTER_GENES.out.adata_filtered )

deconvolution_input = BAYESTME_BLEEDING_CORRECTION.out.adata_corrected
.join( ch_input.map { tuple(it[0], it[2]) } )
.map { tuple(it[0], it[1], it[2], 1000.0, []) }
def deconvolution_input = null

if (params.bleeding_correction) {
BAYESTME_BLEEDING_CORRECTION( BAYESTME_FILTER_GENES.out.adata_filtered )

deconvolution_input = BAYESTME_BLEEDING_CORRECTION.out.adata_corrected
.join( ch_input.map { tuple(it[0], it[2]) } )
.map { tuple(it[0], it[1], it[2], 1000.0, []) }
} else {
deconvolution_input = BAYESTME_FILTER_GENES.out.adata_filtered
.join( ch_input.map { tuple(it[0], it[2]) } )
.map { tuple(it[0], it[1], it[2], 1000.0, []) }
}

BAYESTME_DECONVOLUTION( deconvolution_input )

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7 changes: 6 additions & 1 deletion nextflow/tests/subworkflows/bayestme/bayestme_basic_visium_analysis/test.yml
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@@ -1,5 +1,10 @@
- name: bayestme_basic_visium_analysis
command: nextflow run ./nextflow/tests/subworkflows/bayestme/bayestme_basic_visium_analysis -queue-size 1 -entry bayestme_basic_visium_analysis -c ./nextflow/tests/subworkflows/bayestme/bayestme_basic_visium_analysis/nextflow.config -c ./nextflow/tests/config/nextflow.config
command: nextflow run ./nextflow/tests/subworkflows/bayestme/bayestme_basic_visium_analysis -queue-size 1 -entry bayestme_basic_visium_analysis -c ./nextflow/tests/subworkflows/bayestme/bayestme_basic_visium_analysis/nextflow.config -c ./nextflow/tests/config/nextflow.config --bleeding_correction true
tags:
- bayestme_basic_visium_analysis
files: []
- name: bayestme_basic_visium_analysis_skip_bleeding
command: nextflow run ./nextflow/tests/subworkflows/bayestme/bayestme_basic_visium_analysis -queue-size 1 -entry bayestme_basic_visium_analysis -c ./nextflow/tests/subworkflows/bayestme/bayestme_basic_visium_analysis/nextflow.config -c ./nextflow/tests/config/nextflow.config --bleeding_correction false
tags:
- bayestme_basic_visium_analysis
files: []
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