From 82784295364ffc436afd2cb7ac35258f59763efa Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Wed, 30 Oct 2024 10:13:59 +0000
Subject: [PATCH] also convert concat h5ads

---
 modules/local/concat_h5ad.nf         |  2 +-
 subworkflows/local/mtx_conversion.nf | 19 ++++++++++++-------
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/modules/local/concat_h5ad.nf b/modules/local/concat_h5ad.nf
index 41310553..393a7353 100644
--- 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
index 55bd68dc..9891536d 100644
--- 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)