diff --git a/CHANGELOG.md b/CHANGELOG.md
index 156f76aae3..261730d4a0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- [#1541](https://github.com/nf-core/sarek/pull/1541) - Getting bam and bai published in the same folder
 - [#1542](https://github.com/nf-core/sarek/pull/1542) - Removing legacy configs of `CUSTOM_DUMPSOFTWAREVERSIONS`
 
 ### Removed
diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf
index 0f13d7e424..1d94174476 100644
--- a/workflows/sarek/main.nf
+++ b/workflows/sarek/main.nf
@@ -253,6 +253,12 @@ workflow SAREK {
             }
             .set { reads_grouping_key }
 
+        reads_for_alignment = reads_for_alignment.map{ meta, reads ->
+            // Update meta.id to meta.sample no multiple lanes or splitted fastqs
+            if (meta.size * meta.num_lanes == 1) [ meta + [ id:meta.sample ], reads ]
+            else [ meta, reads ]
+        }
+
         // reads will be sorted
         sort_bam = true
         FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON(reads_for_alignment, index_alignment, sort_bam, fasta, fasta_fai)