Merge branch 'dev' into fix_sortmerna_index

nf-core · Dec 18, 2024 · f449840 · f449840
2 parents ae6990a + 06fa117
commit f449840
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Showing 6 changed files with 12 additions and 3 deletions.
diff --git a/CHANGELOG.md b/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

diff --git a/modules.json b/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": {

diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml
diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test
diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/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)