Patch 2.5.4

.github/workflows/ci.yml

@@ -41,13 +41,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/eager:2.5.3
+        run: docker build --no-cache . -t nfcore/eager:2.5.4
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:2.5.3
+          docker tag nfcore/eager:dev nfcore/eager:2.5.4
       - name: Install Nextflow
         env:
           CAPSULE_LOG: none
@@ -222,4 +222,4 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_mtnucratio
       - name: RESCALING Run basic pipeline with basic pipeline but with mapDamage rescaling of BAM files. Note this will be slow
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_mapdamage_rescaling --run_genotyping --genotyping_tool hc --genotyping_source 'rescaled'
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_mapdamage_rescaling --run_genotyping --genotyping_tool hc --genotyping_source 'rescaled'

.github/workflows/linting_comment.yml

@@ -1,4 +1,3 @@
-
 name: nf-core linting comment
 # This workflow is triggered after the linting action is complete
 # It posts an automated comment to the PR, even if the PR is coming from a fork
@@ -12,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@v2
+        uses: dawidd6/action-download-artifact@v6
         with:
           workflow: linting.yml
 
@@ -26,4 +25,3 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
           path: linting-logs/lint_results.md
-

CHANGELOG.md

@@ -3,6 +3,18 @@
 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).
 
+## [2.5.4] - 2025-09-05
+
+### `Added`
+
+### `Fixed`
+
+- Corrected the citation for the default values used in `bwaalnn` and `bwaalnk` stated in the documentation (♥ to @meret-haeusler reporting, fix by @jfy133).
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## [2.5.3] - 2025-03-18
 
 ### `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-2.5.3/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.5.4/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.5.3 > nf-core-eager-2.5.3.yml
+RUN conda env export --name nf-core-eager-2.5.4 > nf-core-eager-2.5.4.yml

README.md

@@ -15,6 +15,8 @@
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23eager-4A154B?logo=slack)](https://nfcore.slack.com/channels/eager)
 
+![HiRSE Code Promo Badge](https://img.shields.io/badge/Promo-8db427?label=HiRSE&labelColor=005aa0&link=https%3A%2F%2Fgo.fzj.de%2FCodePromo) 
+
 >[!IMPORTANT]  
 > nf-core/eager versions 2.* are only compatible with Nextflow versions up to 22.10.6!
 

environment.yml

@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-eager-2.5.3
+name: nf-core-eager-2.5.4
 channels:
   - conda-forge
   - bioconda

nextflow.config

@@ -289,7 +289,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/eager:2.5.3'
+process.container = 'nfcore/eager:2.5.4'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -419,7 +419,7 @@ manifest {
   description = 'A fully reproducible and state-of-the-art ancient DNA analysis pipeline'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.07.1'
-  version = '2.5.3'
+  version = '2.5.4'
 }
 
 // Function to ensure that resource requirements don't go beyond