Merge branch 'ensure_notnull_pseudo' of github.com:nf-core/rnaseq into ensure_notnull_pseudo

Author: pinin4fjords

CHANGELOG.md

@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [PR #1123](https://github.com/nf-core/rnaseq/pull/1123) - Overhaul tximport.r, output length tables
 - [PR #1124](https://github.com/nf-core/rnaseq/pull/1124) - Ensure pseudoaligner is set if pseudoalignment is not skipped
+- [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
 

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
     //