diff --git a/CHANGELOG.md b/CHANGELOG.md
index 97f8c99e..ecff842f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,6 @@
# nf-core/methylseq
-## v2.6.0dev - [date]
+## [v2.6.0](https://github.com/nf-core/methylseq/releases/tag/2.6.0) - 2024-01-05
### Bug fixes & refactoring
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index ad28ec5b..c6e99955 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
report_comment: >
- This report has been generated by the nf-core/methylseq
+ This report has been generated by the nf-core/methylseq
analysis pipeline. For information about how to interpret these results, please see the
- documentation.
+ documentation.
report_section_order:
"nf-core-methylseq-methods-description":
order: -1000
diff --git a/nextflow.config b/nextflow.config
index 5bdfa5e9..d95f12b2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -297,7 +297,7 @@ manifest {
description = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community."""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
- version = '2.6.0dev'
+ version = '2.6.0'
doi = '10.5281/zenodo.1343417'
}
diff --git a/tests/pipeline/bismark/main.nf.test.snap b/tests/pipeline/bismark/main.nf.test.snap
index 3d2247c3..281ff290 100644
--- a/tests/pipeline/bismark/main.nf.test.snap
+++ b/tests/pipeline/bismark/main.nf.test.snap
@@ -1,21 +1,21 @@
{
"single_end_software_versions": {
"content": [
- "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}"
+ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}"
],
- "timestamp": "2024-01-05T14:14:17.281822498"
+ "timestamp": "2024-01-05T13:33:44.592961646"
},
"single_end_nomeseq_software_versions": {
"content": [
- "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}"
+ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}"
],
- "timestamp": "2024-01-05T14:21:31.783610175"
+ "timestamp": "2024-01-05T13:38:45.868954182"
},
"single_end_rrbs_software_versions": {
"content": [
- "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}"
+ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0}}"
],
- "timestamp": "2024-01-05T14:17:51.992881339"
+ "timestamp": "2024-01-05T13:36:19.58008405"
},
"single_end_nomeseq": {
"content": [
@@ -55,9 +55,9 @@
},
"clip_r1_software_versions": {
"content": [
- "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}"
+ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}"
],
- "timestamp": "2024-01-05T14:23:04.466332751"
+ "timestamp": "2024-01-05T13:39:54.162519593"
},
"single_end": {
"content": [
diff --git a/tests/pipeline/bismark_hisat/main.nf.test.snap b/tests/pipeline/bismark_hisat/main.nf.test.snap
index cd71725a..07d914d9 100644
--- a/tests/pipeline/bismark_hisat/main.nf.test.snap
+++ b/tests/pipeline/bismark_hisat/main.nf.test.snap
@@ -1,15 +1,15 @@
{
"single_end_software_versions": {
"content": [
- "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}"
+ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}"
],
- "timestamp": "2024-01-05T14:28:08.815211757"
+ "timestamp": "2024-01-05T13:41:11.426077518"
},
"single_end_rrbs_software_versions": {
"content": [
- "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}"
+ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0}}"
],
- "timestamp": "2024-01-05T14:33:15.277969284"
+ "timestamp": "2024-01-05T13:43:52.561148623"
},
"single_end": {
"content": [
diff --git a/tests/pipeline/bwameth/main.nf.test.snap b/tests/pipeline/bwameth/main.nf.test.snap
index 20296008..fccd1fc2 100644
--- a/tests/pipeline/bwameth/main.nf.test.snap
+++ b/tests/pipeline/bwameth/main.nf.test.snap
@@ -1,15 +1,15 @@
{
"single_end_software_versions": {
"content": [
- "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}"
+ "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}"
],
- "timestamp": "2024-01-05T14:41:25.742050491"
+ "timestamp": "2024-01-05T13:46:07.95961601"
},
"single_end_rrbs_software_versions": {
"content": [
- "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}"
+ "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0}}"
],
- "timestamp": "2024-01-05T14:44:15.01614543"
+ "timestamp": "2024-01-05T13:47:24.172597347"
},
"single_end": {
"content": [