Merge branch 'dev' into fix_sortmerna_index

Author: pinin4fjords

CHANGELOG.md

@@ -19,6 +19,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1463](https://github.com/nf-core/rnaseq/pull/1463) - Move channel operations outside of the onComplete() block
 - [PR #1467](https://github.com/nf-core/rnaseq/pull/1467) - Add test suite for UMI handling functionality
 - [PR #1466](https://github.com/nf-core/rnaseq/pull/1466) - Factor out UMI handling
+- [PR #1470](https://github.com/nf-core/rnaseq/pull/1470) - Update subworkflow to account for fix to bad argument handling
 - [PR #1469](https://github.com/nf-core/rnaseq/pull/1469) - Minor docs fix
 - [PR #1459](https://github.com/nf-core/rnaseq/pull/1466) - Remove reference to unused "skip_sample_count" value in email templates
 - [PR #1471](https://github.com/nf-core/rnaseq/pull/1471) - Fix prepare_genome subworkflow for sortmerna

modules.json

@@ -363,7 +363,7 @@
                     },
                     "fastq_qc_trim_filter_setstrandedness": {
                         "branch": "master",
-                        "git_sha": "2c0260ed80daeca9c6dfa477a4daf04ff336dc37",
+                        "git_sha": "8a01490596dbe8443bd6bc6ae4207ae9485f33e3",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_subsample_fq_salmon": {

subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf

@@ -155,7 +155,8 @@ workflow RNASEQ {
         params.umi_discard_read,
         params.stranded_threshold,
         params.unstranded_threshold,
-        params.skip_linting
+        params.skip_linting,
+        false
     )
 
     ch_multiqc_files                  = ch_multiqc_files.mix(FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS.out.multiqc_files)