From e3cb3d950d91e20ec0154b4833a728a46a6f5585 Mon Sep 17 00:00:00 2001
From: ch99l <chinhaolee10@gmail.com>
Date: Mon, 12 Oct 2026 15:26:26 +0800
Subject: [PATCH] v0.10.4: include filtered BAM for visium and visium-hd in
 output directory

---
 CHANGELOG.md                                        |  5 +++++
 README.md                                           | 10 ++++++++--
 modules/prepare_input/shared/filter_barcoded_bam.nf |  2 +-
 nextflow.config                                     |  2 +-
 4 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 07e9034..046b6b7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,11 @@ This file contains all notable changes to Bambu-Pipe.
 
 ---
 
+## [v0.10.4] - 2026-10-12
+
+### Changed
+- The filtered BAM produced for Visium and Visium HD samples (`<sample>_filtered.bam` and `.bai`) is now always published to `bam/`, instead of `intermediate_bam/` only with `--save_intermediates`
+
 ## [v0.10.3] - 2026-10-01
 
 ### Changed
diff --git a/README.md b/README.md
index 90a5c53..bf904a5 100644
--- a/README.md
+++ b/README.md
@@ -293,8 +293,10 @@ output/
 │
 ├── bam/
 │   ├── <sample>_demultiplexed.bam
-│   └── <sample>_demultiplexed.bam.bai
-│    # (one pair per sample for multi-sample runs)
+│   ├── <sample>_demultiplexed.bam.bai
+│   ├── <sample>_filtered.bam        # Visium samples only (out-of-tissue reads removed)
+│   └── <sample>_filtered.bam.bai
+│    # (for multi-sample runs, each sample has its own .bam and .bai)
 │
 ├── extended_annotations.gtf
 │
@@ -355,6 +357,10 @@ output/
 │
 ├── pipeline_info/
 │
+├── bam/
+│   ├── <sample>_filtered.bam        # out-of-tissue reads removed
+│   └── <sample>_filtered.bam.bai
+│
 ├── extended_annotations.gtf
 │
 ├── unique_counts/
diff --git a/modules/prepare_input/shared/filter_barcoded_bam.nf b/modules/prepare_input/shared/filter_barcoded_bam.nf
index a7fc3a8..29c668a 100644
--- a/modules/prepare_input/shared/filter_barcoded_bam.nf
+++ b/modules/prepare_input/shared/filter_barcoded_bam.nf
@@ -1,5 +1,5 @@
 process FILTER_BARCODED_BAM {
-    publishDir "$params.output_dir/intermediate_bam", mode: 'copy', pattern: '*_filtered.bam*', enabled: params.save_intermediates
+    publishDir "${params.output_dir}/bam", mode: 'copy', pattern: '*_filtered.bam*'
     label "minimap2_samtools"
     label "medium_cpu"
     label "medium_mem"
diff --git a/nextflow.config b/nextflow.config
index 22b638f..44eb1c4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -2,7 +2,7 @@ manifest {
     name        = 'Bambu-Pipe'
     description = 'Context-aware transcript quantification from long-read single-cell and spatial transcriptomics data'
     author      = 'Andre Sim, Chin Hao Lee, Min Hao Ling'
-    version     = 'v0.10.3'
+    version     = 'v0.10.4'
     mainScript  = 'main.nf'
     nextflowVersion = '!>=26.04.0'
 }