diff --git a/CHANGELOG.md b/CHANGELOG.md
index c93a8f724..a1a6fe5b8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1206](https://github.com/nf-core/rnaseq/pull/1206) - Remove `lib/` directory and `modules.config`
 - [PR #1212](https://github.com/nf-core/rnaseq/pull/1212) - Update all modules and subworkflows to latest versions
 - [PR #1210](https://github.com/nf-core/rnaseq/pull/1210) - Use pseudoalignment subworkflow components from nf-core/modules
+- [PR #1213](https://github.com/nf-core/rnaseq/pull/1213) - Pass transcriptome fasta through to samtools stats
 
 ### Parameters
 
diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf
index c62ca66bd..1b88ed2e5 100755
--- a/workflows/rnaseq/main.nf
+++ b/workflows/rnaseq/main.nf
@@ -334,7 +334,7 @@ workflow NFCORE_RNASEQ {
             // Co-ordinate sort, index and run stats on transcriptome BAM
             BAM_SORT_STATS_SAMTOOLS (
                 ch_transcriptome_bam,
-                ch_fasta.map { [ [:], it ] }
+                ch_transcript_fasta.map { [ [:], it ] }
             )
             ch_transcriptome_sorted_bam = BAM_SORT_STATS_SAMTOOLS.out.bam
             ch_transcriptome_sorted_bai = BAM_SORT_STATS_SAMTOOLS.out.bai