Merge pull request #1124 from nf-core/ensure_notnull_pseudo

Ensure pseudoaligner is set if pseudoalignment is not skipped

Author: pinin4fjords

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}")

conf/modules.config

@@ -1087,7 +1087,6 @@ if (!params.skip_multiqc) {
 
 if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
     process {
-
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT' {
             ext.args   = { params.extra_salmon_quant_args ?: '' }
             publishDir = [
@@ -1112,7 +1111,7 @@ if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'kallisto') {
     }
 }
 
-if (!params.skip_pseudo_alignment) {
+if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
     process {
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TX2GENE' {
             publishDir = [

nextflow.config

@@ -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

@@ -816,9 +816,8 @@ workflow RNASEQ {
     //
     ch_pseudo_multiqc                   = Channel.empty()
     ch_pseudoaligner_pca_multiqc        = Channel.empty()
-    ch_pseudoaligner_clustering_multiqc = Channel.empty()
-    
-    if (!params.skip_pseudo_alignment) {
+    ch_pseudoaligner_clustering_multiqc = Channel.empty()    
+    if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
 
        if (params.pseudo_aligner == 'salmon') {
            ch_pseudo_index = PREPARE_GENOME.out.salmon_index