Merge pull request #343 from nf-core/fix-mirdeep-out-bump-versions

Fix-mirdeep-out-bump-versions
nf-core · Apr 18, 2024 · 3c1eaf8 · 3c1eaf8
2 parents 2741a78 + 3a65e94
commit 3c1eaf8
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,14 +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).
 
-## v2.3.1 - XXXX-XX-XX- Gray Zinc Dalmation Patch
+## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch
 
 - [[#328]](https://github.com/nf-core/smrnaseq/pull/328) - Fix [casting issue](https://github.com/nf-core/smrnaseq/issues/327) in mirtrace module
 - [[#334]](https://github.com/nf-core/smrnaseq/pull/334) - Fix [input channel cardinality](https://github.com/nf-core/smrnaseq/issues/331) in `MIRDEEP2_RUN` module
 - [[#334]](https://github.com/nf-core/smrnaseq/pull/334) - Fix [bowtie conda version](https://github.com/nf-core/smrnaseq/issues/333) in `BOWTIE_MAP_SEQ` module
 - [[#335]](https://github.com/nf-core/smrnaseq/pull/335) - Final fix for [casting issue](https://github.com/nf-core/smrnaseq/issues/327) in mirtrace module
 - [[#337]](https://github.com/nf-core/smrnaseq/pull/337) - Fix [three_prime_adapter issue](https://github.com/nf-core/smrnaseq/issues/326), allow `auto-detect` as value
 - [[#342]](https://github.com/nf-core/smrnaseq/pull/342) - Fix [phred offset issue](https://github.com/nf-core/smrnaseq/issues/341), allow specifying phred offset for FASTQ files
+- [[#343]](https://github.com/nf-core/smrnaseq/pull/343) - Fix [mirdeep2 output missing](https://github.com/nf-core/smrnaseq/issues/330), fix mirdeep2 outputs missing in outdir
 
 ### Software dependencies
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/smrnaseq/tree/dev" target="_blank">nf-core/smrnaseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/smrnaseq/releases/tag/2.3.1" target="_blank">nf-core/smrnaseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/smrnaseq/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/smrnaseq/2.3.1/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-smrnaseq-methods-description":

diff --git a/conf/modules.config b/conf/modules.config
@@ -329,14 +329,14 @@ process {
     //
     // MIRDEEP
     //
-    withName: 'MIRDEEP2_MAPPER' {
+    withName: 'NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_MAPPER' {
         publishDir = [
             path: { "${params.outdir}/mirdeep2/mapper" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: 'MIRDEEP2_RUN' {
+    withName: 'NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN' {
         publishDir = [
             path: { "${params.outdir}/mirdeep2/run" },
             mode: params.publish_dir_mode,

diff --git a/nextflow.config b/nextflow.config
@@ -308,7 +308,7 @@ manifest {
     description     = """Small RNA-Seq Best Practice Analysis Pipeline."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.3.1dev'
+    version         = '2.3.1'
     doi             = '10.5281/zenodo.3456879'
 }