diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4680c417a..38d6bfb30 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,11 +3,18 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## dev
+
+### Enhancements and fixes
+
+- [PR #1126](https://github.com/nf-core/rnaseq/pull/1126) - Fixes error when transcript_fasta not provided and skip_gtf_filter set to true
+- [#1125](https://github.com/nf-core/rnaseq/issues/1125) - Pipeline fails if transcript_fasta not provided and skip_gtf_filter = true
+
 ## [[3.13.1](https://github.com/nf-core/rnaseq/releases/tag/3.13.1)] - 2023-11-17
 
 ### Enhancements and fixes
 
-- [[PR #1121](https://github.com/nf-core/rnaseq/pull/1121) - Changes for 3.13.1 patch release incl. igenomes star fix
+- [PR #1121](https://github.com/nf-core/rnaseq/pull/1121) - Changes for 3.13.1 patch release incl. igenomes star fix
 
 ## [[3.13.0](https://github.com/nf-core/rnaseq/releases/tag/3.13.0)] - 2023-11-17
 
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 0be947954..0840c7734 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -47,7 +47,7 @@ workflow PREPARE_GENOME {
     rsem_index           // directory: /path/to/rsem/index/
     salmon_index         // directory: /path/to/salmon/index/
     kallisto_index       // directory: /path/to/kallisto/index/
-    hisat2_index         // directory: /path/to/hisat2/index/ 
+    hisat2_index         // directory: /path/to/hisat2/index/
     bbsplit_index        // directory: /path/to/rsem/index/
     gencode              //   boolean: whether the genome is from GENCODE
     is_aws_igenome       //   boolean: whether the genome files are from AWS iGenomes
@@ -139,14 +139,13 @@ workflow PREPARE_GENOME {
         } else {
             ch_transcript_fasta = Channel.value(file(transcript_fasta))
         }
-        if (gencode) { 
+        if (gencode) {
             PREPROCESS_TRANSCRIPTS_FASTA_GENCODE ( ch_transcript_fasta )
             ch_transcript_fasta = PREPROCESS_TRANSCRIPTS_FASTA_GENCODE.out.fasta
             ch_versions         = ch_versions.mix(PREPROCESS_TRANSCRIPTS_FASTA_GENCODE.out.versions)
         }
     } else {
         ch_transcript_fasta = MAKE_TRANSCRIPTS_FASTA ( ch_fasta, ch_gtf ).transcript_fasta
-        ch_versions         = ch_versions.mix(GTF_FILTER.out.versions)
         ch_versions         = ch_versions.mix(MAKE_TRANSCRIPTS_FASTA.out.versions)
     }
 
@@ -268,7 +267,7 @@ workflow PREPARE_GENOME {
             ch_versions     = ch_versions.mix(SALMON_INDEX.out.versions)
         }
     }
-    
+
     //
     // Uncompress Kallisto index or generate from scratch if required
     //