also convert concat h5ads

nf-core · Oct 30, 2024 · 8278429 · 8278429
1 parent 5c31226
commit 8278429
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Showing 2 changed files with 13 additions and 8 deletions.
diff --git a/modules/local/concat_h5ad.nf b/modules/local/concat_h5ad.nf
@@ -11,7 +11,7 @@ process CONCAT_H5AD {
     path samplesheet
 
     output:
-    path "*.h5ad", emit: h5ad
+    tuple val(meta), path("*.h5ad"), emit: h5ad
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/subworkflows/local/mtx_conversion.nf b/subworkflows/local/mtx_conversion.nf
@@ -56,13 +56,6 @@ workflow MTX_CONVERSION {
 
         }
 
-        //
-        // MODULE: Convert to Rds with AnndataR package
-        //
-        ANNDATAR_CONVERT (
-            ch_h5ads
-        )
-
         //
         // Concat sample-specific h5ad in one
         //
@@ -78,6 +71,18 @@ workflow MTX_CONVERSION {
             ch_concat_h5ad_input,
             samplesheet
         )
+        ch_h5ad_concat = CONCAT_H5AD.out.h5ad.map{ meta, file ->
+            def meta_clone = meta.clone()
+            meta_clone.id = 'combined' // maintain output prefix
+            [ meta_clone, file ]
+        }
+
+        //
+        // MODULE: Convert to Rds with AnndataR package
+        //
+        ANNDATAR_CONVERT (
+            ch_h5ads.mix( ch_h5ad_concat )
+        )
 
         //TODO CONCAT h5ad and MTX to h5ad should also have versions.yaml output
         // ch_versions = ch_versions.mix(MTX_TO_H5AD.out.versions, MTX_TO_SEURAT.out.versions)