Merge pull request #1474 from nf-core/prerelease_3.18.0

Bump versions to 3.18.0
nf-core · Dec 19, 2024 · a27ec8e · a27ec8e
2 parents 329fd69 + 0cf9100
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,13 +3,15 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-# 3.18.0dev - xxxx-xx-xx
+# 3.18.0 - 2024-12-19
 
 ### Credits
 
 Special thanks to the following for their contributions to the release:
 
 - [Caitlin Winkler](https://github.com/oligomyeggo)
+- [Jonathan Manning](https://github.com/pinin4fjords)
+- [Maxime Garcia](https://github.com/maxulysse)
 - [Siddhartha Bagaria](https://github.com/siddharthab)
 
 ### Enhancements & fixes
@@ -24,6 +26,15 @@ Special thanks to the following for their contributions to the release:
 - [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
 - [PR #1473](https://github.com/nf-core/rnaseq/pull/1473) - Bump STAR modules
+- [PR #1474](https://github.com/nf-core/rnaseq/pull/1474) - Bump versions to 3.18.0
+
+## Parameters
+
+| Old parameter | New parameter         |
+| ------------- | --------------------- |
+|               | `--skip_linting`      |
+|               | `--extra_fqlint_args` |
+|               | `--umi_dedup_tool`    |
 
 ### Software dependencies
 

diff --git a/nextflow.config b/nextflow.config
@@ -333,7 +333,7 @@ manifest {
     description     = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '3.18.0dev'
+    version         = '3.18.0'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }
 

diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -46,7 +46,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [
@@ -240,7 +240,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [

diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
@@ -46,7 +46,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [
@@ -234,7 +234,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [

diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
@@ -47,7 +47,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [
@@ -237,7 +237,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [

diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap
@@ -59,7 +59,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [
@@ -319,7 +319,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [

diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
@@ -137,7 +137,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [
@@ -1246,7 +1246,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [

diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
@@ -143,7 +143,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [
@@ -1460,7 +1460,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [

diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap
@@ -53,7 +53,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [
@@ -392,7 +392,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [

diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap
@@ -43,7 +43,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [
@@ -182,7 +182,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [

diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
@@ -133,7 +133,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [

diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
@@ -137,7 +137,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [
@@ -1339,7 +1339,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [

diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap
@@ -140,7 +140,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [
@@ -1610,7 +1610,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [
@@ -2747,7 +2747,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.18.0dev"
+                    "nf-core/rnaseq": "v3.18.0"
                 }
             },
             [

diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml
@@ -1,5 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/rnaseq/tree/dev" target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnaseq/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/3.18.0"
+  target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how
+  to interpret these results, please see the <a href="https://nf-co.re/rnaseq/3.18.0/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   # Important checks and failures
   sample-status:
@@ -117,9 +120,9 @@ module_order:
 # Don't show % Dups in the General Stats table (we have this from Picard)
 table_columns_visible:
   "FastQC (raw)":
-    percent_duplicates: False
+    percent_duplicates: false
   "FastQC (trimmed)":
-    percent_duplicates: False
+    percent_duplicates: false
 
 extra_fn_clean_exts:
   - ".umi_dedup"
@@ -216,31 +219,45 @@ sp:
 custom_data:
   fail_trimmed_samples:
     section_name: "WARNING: Fail Trimming Check"
-    description: "List of samples that failed the minimum trimmed reads threshold specified via the '--min_trimmed_reads' parameter, and hence were ignored for the downstream processing steps."
+    description: "List of samples that failed the minimum trimmed reads threshold
+      specified via the '--min_trimmed_reads' parameter, and hence were ignored for
+      the downstream processing steps."
     plot_type: "table"
     pconfig:
       id: "fail_trimmed_samples_table"
       title: "Samples failed trimming threshold"
       namespace: "Samples failed trimming threshold"
   fail_mapped_samples:
     section_name: "WARNING: Fail Alignment Check"
-    description: "List of samples that failed the STAR minimum mapped reads threshold specified via the '--min_mapped_reads' parameter, and hence were ignored for the downstream processing steps."
+    description: "List of samples that failed the STAR minimum mapped reads threshold
+      specified via the '--min_mapped_reads' parameter, and hence were ignored for
+      the downstream processing steps."
     plot_type: "table"
     pconfig:
       id: "fail_mapped_samples_table"
       title: "Samples failed mapping threshold"
       namespace: "Samples failed mapping threshold"
   fail_strand_check:
     section_name: "Strandedness Checks"
-    description: "<p>The strandedness used for analysis in this workflow can either be provided by the user or automatically inferred by <b>Salmon</b> using a sample of reads. In both cases, strandedness is verified at the end of the workflow using <b>RSeQC</b>'s <a href='http://rseqc.sourceforge.net/#infer-experiment-py'>infer_experiment.py</a> on genomic alignments. In this table, a pass indicates a match between the supplied strandedness (or that inferred by Salmon) and RSeQC results. A fail indicates a mismatch or 'undetermined' strandedness. 'Undetermined' strandedness can signal QC issues, including potential genomic DNA contamination.</p><p><b>Note:</b> Rows are duplicated for an 'auto' setting to allow comparison of statistics between inference methods.</p>"
+    description: "<p>The strandedness used for analysis in this workflow can either
+      be provided by the user or automatically inferred by <b>Salmon</b> using a sample
+      of reads. In both cases, strandedness is verified at the end of the workflow
+      using <b>RSeQC</b>'s <a href='http://rseqc.sourceforge.net/#infer-experiment-py'>infer_experiment.py</a>
+      on genomic alignments. In this table, a pass indicates a match between the supplied
+      strandedness (or that inferred by Salmon) and RSeQC results. A fail indicates
+      a mismatch or 'undetermined' strandedness. 'Undetermined' strandedness can signal
+      QC issues, including potential genomic DNA contamination.</p><p><b>Note:</b>
+      Rows are duplicated for an 'auto' setting to allow comparison of statistics
+      between inference methods.</p>"
     plot_type: "table"
     pconfig:
       id: "fail_strand_check_table"
       title: "Samples strandedness check"
       namespace: "Samples strandedness check"
     headers:
       Status:
-        description: Pass if the strandedness inferred by RSeQC matches that provided by the user or predicted by Salmon. Fail otherwise.
+        description: Pass if the strandedness inferred by RSeQC matches that provided
+          by the user or predicted by Salmon. Fail otherwise.
       Strand inference method:
         description: Tool used to detect strandedness
       Provided strandedness: