diff --git a/CHANGELOG.md b/CHANGELOG.md
index ac293d86a..e62628fc6 100644
--- a/CHANGELOG.md
+++ b/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 - [PR #1340](https://github.com/nf-core/rnaseq/pull/1340) - Remove out-of-date Azure specific guidance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
 
diff --git a/modules.json b/modules.json
index 8d89cfcbb..f197e3f65 100644
--- a/modules.json
+++ b/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": {
diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
index cd69166f3..db73488f1 100644
--- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
+++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
@@ -134,7 +134,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
     .mix(ch_fastq.single)
     .set { ch_filtered_reads }
 
-    ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first())
 
     //
     // SUBWORKFLOW: Read QC, extract UMI and trim adapters with TrimGalore!
diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf
index 896159378..7bf5d36e0 100755
--- a/workflows/rnaseq/main.nf
+++ b/workflows/rnaseq/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,