Merge pull request #1345 from nf-core/fix_preprocessing_call

Fix preprocessing call

Author: pinin4fjords

CHANGELOG.md

@@ -105,6 +105,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1340](https://github.com/nf-core/rnaseq/pull/1340) - Remove out-of-date Azure specific guidance
 - [PR #1341](https://github.com/nf-core/rnaseq/pull/1341) - Add rename in the MultiQC report for samples without techreps
 - [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
 
 ### Parameters
 

modules.json

@@ -324,7 +324,7 @@
                     },
                     "fastq_qc_trim_filter_setstrandedness": {
                         "branch": "master",
-                        "git_sha": "b86de50ab60c19ab40e70a4501820f4cb307050b",
+                        "git_sha": "22c8d535286728605ccd229e5d1bb014cb965f8f",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_subsample_fq_salmon": {

subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf

@@ -139,7 +139,7 @@ workflow RNASEQ {
         params.skip_fastqc || params.skip_qc,
         params.skip_trimming,
         params.skip_umi_extract,
-        !params.salmon_index && params.pseudo_aligner == 'salmon' && !skip_pseudo_alignment,
+        !params.salmon_index && params.pseudo_aligner == 'salmon' && !params.skip_pseudo_alignment,
         !params.sortmerna_index && params.remove_ribo_rna,
         params.trimmer,
         params.min_trimmed_reads,