diff --git a/CHANGELOG.md b/CHANGELOG.md
index c27d1b8d8..cb3b78e7a 100644
--- 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
index bc528efed..aacf937c3 100644
--- 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
index 083846538..8fdef2729 100644
--- 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
index e2fb3b4bf..96f7b3778 100644
--- 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
index 3c943fb61..e765de22a 100644
--- 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
index d3a458f5d..192ddaedc 100644
--- 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
index 1b0b0c03f..7c0412a2e 100644
--- 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
index 0de885b42..6abd45320 100644
--- 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
index fd9043460..87a9a3e14 100644
--- 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
index c93205278..0c6fd0e1c 100644
--- 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
index 4f89bd3f0..7a9edbf1b 100644
--- 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
index 2b1b7eca7..ab6ed8d6c 100644
--- 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
index 5c9f34cb0..4e153a33b 100644
--- 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
index 9b8ee731a..4af07dc67 100644
--- 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 nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation.
+ This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how
+ to interpret these results, please see the documentation.
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"
@@ -216,7 +219,9 @@ 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"
@@ -224,7 +229,9 @@ custom_data:
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"
@@ -232,7 +239,16 @@ custom_data:
namespace: "Samples failed mapping threshold"
fail_strand_check:
section_name: "Strandedness Checks"
- description: "The strandedness used for analysis in this workflow can either be provided by the user or automatically inferred by Salmon using a sample of reads. In both cases, strandedness is verified at the end of the workflow using RSeQC's infer_experiment.py 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.
Note: Rows are duplicated for an 'auto' setting to allow comparison of statistics between inference methods.
"
+ description: "The strandedness used for analysis in this workflow can either
+ be provided by the user or automatically inferred by Salmon using a sample
+ of reads. In both cases, strandedness is verified at the end of the workflow
+ using RSeQC's infer_experiment.py
+ 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.
Note:
+ Rows are duplicated for an 'auto' setting to allow comparison of statistics
+ between inference methods.
"
plot_type: "table"
pconfig:
id: "fail_strand_check_table"
@@ -240,7 +256,8 @@ custom_data:
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: