diff --git a/bin/clustering.qmd b/bin/clustering.qmd index 671471c..8c62585 100644 --- a/bin/clustering.qmd +++ b/bin/clustering.qmd @@ -1,6 +1,5 @@ --- -title: "nf-core/spatialvi" -subtitle: "Dimensionality reduction and clustering" +title: "Dimensionality reduction and clustering" format: nf-core-html: default jupyter: python3 diff --git a/bin/quality_controls.qmd b/bin/quality_controls.qmd index 6bfe9c3..784ec78 100644 --- a/bin/quality_controls.qmd +++ b/bin/quality_controls.qmd @@ -1,6 +1,5 @@ --- -title: "nf-core/spatialvi" -subtitle: "Pre-processing and quality controls" +title: "Pre-processing and quality controls" format: nf-core-html: default jupyter: python3 diff --git a/bin/spatially_variable_genes.qmd b/bin/spatially_variable_genes.qmd index 6d52c92..5adc45e 100644 --- a/bin/spatially_variable_genes.qmd +++ b/bin/spatially_variable_genes.qmd @@ -1,6 +1,5 @@ --- -title: "nf-core/spatialvi" -subtitle: "Neighborhood enrichment analysis and Spatially variable genes" +title: "Neighborhood enrichment analysis and Spatially variable genes" format: nf-core-html: default jupyter: python3 diff --git a/conf/modules.config b/conf/modules.config index 6740b30..4ec1fbf 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -57,6 +57,7 @@ process { withName: 'READ_DATA|QUALITY_CONTROLS|CLUSTERING|SPATIALLY_VARIABLE_GENES' { ext.prefix = { "${notebook.baseName}" } + ext.args = { "--metadata subtitle:'Sample: ${meta.id}'" } publishDir = [ [ path: { "${params.outdir}/${meta.id}/reports" }, diff --git a/subworkflows/local/downstream.nf b/subworkflows/local/downstream.nf index a477bbc..4f6d742 100644 --- a/subworkflows/local/downstream.nf +++ b/subworkflows/local/downstream.nf @@ -9,7 +9,7 @@ include { QUARTONOTEBOOK as CLUSTERING } from '../../modules/nf-co workflow DOWNSTREAM { take: - sdata_raw + sdata_raw // Channel: [ meta, zarr ] main: