Ensure pseudoaligner is set if pseudoalignment is not skipped

CHANGELOG.md

@@ -3,12 +3,22 @@
 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
+## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21
 
-### Enhancements and fixes
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Jonathan Manning](https://github.com/pinin4fjords)
+- [Regina Hertfelder Reynolds](https://github.com/RHReynolds)
+- [Matthias Zepper](https://github.com/MatthiasZepper)
+
+### Enhancements & fixes
 
-- [[PR #1126](https://github.com/nf-core/rnaseq/pull/1126)] [[#1125](https://github.com/nf-core/rnaseq/issues/1125)] - Pipeline fails if transcript_fasta not provided and `skip_gtf_filter = true`.
-- [[PR #1127](https://github.com/nf-core/rnaseq/pull/1127)] - Enlarge sampling to determine the number of columns in `filter_gtf.py` script.
+- [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) - Pipeline fails if transcript_fasta not provided and `skip_gtf_filter = true`.
+- [PR #1127](https://github.com/nf-core/rnaseq/pull/1127) - Enlarge sampling to determine the number of columns in `filter_gtf.py` script.
 
 ## [[3.13.1](https://github.com/nf-core/rnaseq/releases/tag/3.13.1)] - 2023-11-17
 

bin/filter_gtf.py

@@ -30,7 +30,7 @@ def tab_delimited(file: str) -> float:
 def filter_gtf(fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_id_check: bool) -> None:
     """Filter GTF file based on FASTA sequence names."""
     if tab_delimited(gtf_in) != 8:
-        raise ValueError("Invalid GTF file: Expected nine tab-separated columns.")
+        raise ValueError("Invalid GTF file: Expected 9 tab-separated columns.")
 
     seq_names_in_genome = extract_fasta_seq_names(fasta)
     logger.info(f"Extracted chromosome sequence names from {fasta}")

nextflow.config

@@ -58,7 +58,7 @@ params {
 
     // Alignment
     aligner                    = 'star_salmon'
-    pseudo_aligner             = null
+    pseudo_aligner             = 'salmon'
     seq_center                 = null
     bam_csi_index              = false
     star_ignore_sjdbgtf        = false
@@ -317,7 +317,7 @@ manifest {
     description     = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '3.13.1'
+    version         = '3.13.2'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }
 

workflows/rnaseq.nf

@@ -37,7 +37,13 @@ if (!params.skip_bbsplit && !params.bbsplit_index && params.bbsplit_fasta_list)
 def prepareToolIndices  = []
 if (!params.skip_bbsplit) { prepareToolIndices << 'bbsplit' }
 if (!params.skip_alignment) { prepareToolIndices << params.aligner }
-if (!params.skip_pseudo_alignment && params.pseudo_aligner) { prepareToolIndices << params.pseudo_aligner }
+if (!params.skip_pseudo_alignment) {
+    if(params.pseudo_aligner) { 
+        prepareToolIndices << params.pseudo_aligner 
+    } else {
+        exit 1, "--skip_pseudo_alignment not set, but --pseudo_aligner not set"
+    }
+}
 
 // Determine whether to filter the GTF or not
 def filterGtf =