Merge branch 'dev' into harmonize_new_for_multiqc

Author: pinin4fjords

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 Special thanks to the following for their contributions to the release:
 
 - [Adam Talbot](https://github.com/adamrtalbot)
+- [David Carlson](https://github.com/davidecarlson)
 - [Edmund Miller](https://github.com/edmundmiller)
 - [Jonathan Manning](https://github.com/pinin4fjords)
 - [Laramie Lindsey](https://github.com/laramiellindsey)
@@ -107,6 +108,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1342](https://github.com/nf-core/rnaseq/pull/1342) - Factor out preprocessing
 - [PR #1345](https://github.com/nf-core/rnaseq/pull/1345) - Fix preprocessing call
 - [PR #1350](https://github.com/nf-core/rnaseq/pull/1350) - Reduce resource usage for sort process in bedtools/genomecov
+- [PR #1353](https://github.com/nf-core/rnaseq/pull/1353) - Correct conditional for salmon indexing in preprocessing workflow
 - [PR #1352](https://github.com/nf-core/rnaseq/pull/1352) - Assorted fixes to MultiQC usage
 
 ### Parameters

workflows/rnaseq/main.nf

@@ -128,6 +128,10 @@ workflow RNASEQ {
     // Run RNA-seq FASTQ preprocessing subworkflow
     //
 
+    // The subworkflow only has to do Salmon indexing if it discovers 'auto'
+    // samples, and if we haven't already made one elsewhere
+    salmon_index_available = params.salmon_index || (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon')
+
     FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS (
         ch_fastq,
         ch_fasta,
@@ -141,7 +145,7 @@ workflow RNASEQ {
         params.skip_fastqc || params.skip_qc,
         params.skip_trimming,
         params.skip_umi_extract,
-        !params.salmon_index && params.pseudo_aligner == 'salmon' && !params.skip_pseudo_alignment,
+        !salmon_index_available,
         !params.sortmerna_index && params.remove_ribo_rna,
         params.trimmer,
         params.min_trimmed_reads,