Merge pull request #936 from nf-core/patch

Patch 2.4.6

Author: TCLamnidis

.github/workflows/ci.yml

@@ -37,13 +37,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/eager:2.4.5
+        run: docker build --no-cache . -t nfcore/eager:2.4.6
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:2.4.5
+          docker tag nfcore/eager:dev nfcore/eager:2.4.6
 
       - name: Install Nextflow
         env:

CHANGELOG.md

@@ -3,7 +3,30 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [2.4.5] - 2022-07-39
+## [2.4.6] - 2022-11-14
+
+### `Added`
+
+- [#933](https://github.com/nf-core/eager/issues/933) Added support for customising --seq-length in mapDamage rescaling (♥ to @ashildv for requesting)
+
+### `Fixed`
+
+- Changed endors.py license from GPL to MIT (♥ to @aidaanva for fixing)
+- Removed erroneous R2 in single-end example in input TSV of usage docs (♥ to @aidaanva for fixing)
+- [#928](https://github.com/nf-core/eager/issues/928) Fixed read group incompatibility by re-adding picard AddOrReplaceReadGroups for MultiVCFAnalyzer (♥ to @aidaanva, @meganemichel for reporting)
+- Fixed edge case of DamageProfiler occasionally requiring FASTA index (♥ to @asmaa-a-abdelwahab for reporting)
+- [#834](https://github.com/nf-core/eager/issues/834) Increased significance values in general stats table for Qualimap mean/median coverages (♥ to @neija2611 for reporting)
+- Fixed parameter documentation for `--snpcapture_bed` regarding on-target SNP stats to state these stats currently not displayed in MultiQC only in the Qualimap results (♥ to @meganemichel and @TCLamnidis for reporting)
+- [#934](https://github.com/nf-core/eager/issues/934) Fixed broken parameter setting in mapDamage2 rescale length (♥ to @ashildv for reporting)
+
+### `Dependencies`
+
+- Updated MultiQC to official 1.13 version (rather than alpha)
+- Added pinned MALT dependency to ensure working version in future versions of eager
+
+### `Deprecated`
+
+## [2.4.5] - 2022-08-02
 
 ### `Added`
 

Dockerfile

@@ -7,7 +7,7 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-eager-2.4.5/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.4.6/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.4.5 > nf-core-eager-2.4.5.yml
+RUN conda env export --name nf-core-eager-2.4.6 > nf-core-eager-2.4.6.yml

README.md

@@ -160,29 +160,36 @@ of this pipeline:
 
 Those who have provided conceptual guidance, suggestions, bug reports etc.
 
+* [Alex Hübner](https://github.com/alexhbnr)
 * [Alexandre Gilardet](https://github.com/alexandregilardet)
 * Arielle Munters
 * [Åshild Vågene](https://github.com/ashildv)
+* [Asmaa Ali](https://github.com/asmaa-a-abdelwahab)
 * [Charles Plessy](https://github.com/charles-plessy)
 * [Elina Salmela](https://github.com/esalmela)
+* [Fabian Lehmann](https://github.com/Lehmann-Fabian)
+* [He Yu](https://github.com/paulayu)
 * [Hester van Schalkwyk](https://github.com/hesterjvs)
 * [Ido Bar](https://github.com/IdoBar)
 * [Irina Velsko](https://github.com/ivelsko)
 * [Işın Altınkaya](https://github.com/isinaltinkaya)
 * [Johan Nylander](https://github.com/nylander)
+* [Jonas Niemann](https://github.com/NiemannJ)
 * [Katerine Eaton](https://github.com/ktmeaton)
 * [Kathrin Nägele](https://github.com/KathrinNaegele)
+* [Kevin Lord](https://github.com/lordkev)
+* [Laura Lacher](https://github.com/neija2611)
 * [Luc Venturini](https://github.com/lucventurini)
+* [Mahesh Binzer-Panchal](https://github.com/mahesh-panchal)
 * [Marcel Keller](https://github.com/marcel-keller)
 * [Megan Michel](https://github.com/meganemichel)
 * [Pierre Lindenbaum](https://github.com/lindenb)
 * [Pontus Skoglund](https://github.com/pontussk)
 * [Raphael Eisenhofer](https://github.com/EisenRa)
 * [Roberta Davidson](https://github.com/roberta-davidson)
-* [Torsten Günter](https://bitbucket.org/tguenther/)
-* [Kevin Lord](https://github.com/lordkev)
-* [He Yu](https://github.com/paulayu)
+* [Rodrigo Barquera](https://github.com/RodrigoBarquera)
 * [Selina Carlhoff](https://github.com/scarlhoff)
+* [Torsten Günter](https://bitbucket.org/tguenther)
 
 If you've contributed and you're missing in here, please let us know and we will add you in of course!