From 75879590b1ff57e44e8c97f9489eb1b007d554f9 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Tue, 2 Jun 2026 08:48:20 +0100
Subject: [PATCH] fix(qpx): emit dataset as qpx_output/* files instead of a
 directory

Emit the QPX Parquet dataset as individual files (`qpx_output/*`) rather
than the `qpx_output/` directory. This lets downstream pipelines publish the
dataset files flat (e.g. into a single `qpx/` results folder alongside the
`.h5mu`) via a `publishDir` saveAs, instead of being forced to keep an
intermediate `qpx_output/` subdirectory.

The stub still produces a single `qpx_output/stub.parquet`, so the existing
stub test (qpx_dataset.size() == 1) is unaffected.
---
 modules/bigbio/qpx/main.nf  | 2 +-
 modules/bigbio/qpx/meta.yml | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/bigbio/qpx/main.nf b/modules/bigbio/qpx/main.nf
index 726351f..b96456b 100644
--- a/modules/bigbio/qpx/main.nf
+++ b/modules/bigbio/qpx/main.nf
@@ -16,7 +16,7 @@ process QPX_EXPORT {
     val(project_accession)
 
     output:
-    path "qpx_output/" , emit: qpx_dataset
+    path "qpx_output/*", emit: qpx_dataset
     path "*.h5mu"      , emit: mudata
     path "versions.yml", emit: versions
 
diff --git a/modules/bigbio/qpx/meta.yml b/modules/bigbio/qpx/meta.yml
index 837f3b8..9e5a35a 100644
--- a/modules/bigbio/qpx/meta.yml
+++ b/modules/bigbio/qpx/meta.yml
@@ -41,10 +41,10 @@ input:
       description: PRIDE project accession (e.g. PXD026600) used as output prefix
 output:
   qpx_dataset:
-    - "qpx_output/":
-        type: directory
-        description: QPX Parquet dataset directory
-        pattern: "qpx_output/"
+    - "qpx_output/*":
+        type: file
+        description: QPX Parquet dataset files
+        pattern: "qpx_output/*"
   mudata:
     - "*.h5mu":
         type: file