Merge pull request #87 from nf-core/report-sample-names

Report sample names
nf-core · Oct 11, 2024 · 7c25f5f · 7c25f5f
2 parents a353aae + f0a8a10
commit 7c25f5f
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Showing 5 changed files with 5 additions and 7 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -9,7 +9,7 @@ include { QUARTONOTEBOOK as CLUSTERING               } from '../../modules/nf-co
 workflow DOWNSTREAM {
 
     take:
-    sdata_raw
+    sdata_raw // Channel: [ meta, zarr ]
 
     main:
-Original file line number
+Diff line change
@@ Expand Up @@
     workflow DOWNSTREAM {
         take:
-        sdata_raw
+        sdata_raw // Channel: [ meta, zarr ]
         main:
@@ Expand Down @@