Merge pull request #984 from nf-core/patch

2.4.7 Patch

.github/workflows/ci.yml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['20.07.1', '']
+        nxf_ver: ['20.07.1', '22.10.6']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -37,13 +37,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/eager:2.4.6
+        run: docker build --no-cache . -t nfcore/eager:2.4.7
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:2.4.6
+          docker tag nfcore/eager:dev nfcore/eager:2.4.7
 
       - name: Install Nextflow
         env:
@@ -216,4 +216,4 @@ 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'

CHANGELOG.md

@@ -3,6 +3,21 @@
 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).
 
+## [2.4.7] - 2023-05-16
+
+### `Added`
+
+### `Fixed`
+
+- [#983](https://github.com/nf-core/eager/issues/983) Bump `pygments` version due to incompatibility with MultiQC dependencies (♥ to @MinLuke for reporting)
+
+### `Dependencies`
+
+- `pygments`: 2.9 -> 2.14
+- `multiqc`: 1.13 -> 1.14
+
+### `Deprecated`
+
 ## [2.4.6] - 2022-11-14
 
 ### `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-2.4.6/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.4.7/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.4.6 > nf-core-eager-2.4.6.yml
+RUN conda env export --name nf-core-eager-2.4.7 > nf-core-eager-2.4.7.yml

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-2.4.6
+name: nf-core-eager-2.4.7
 channels:
   - conda-forge
   - bioconda
@@ -9,7 +9,7 @@ dependencies:
   - conda-forge::python=3.9.4
   - conda-forge::markdown=3.3.4
   - conda-forge::pymdown-extensions=8.2
-  - conda-forge::pygments=2.9.0
+  - conda-forge::pygments=2.14.0
   - bioconda::rename=1.601
   - conda-forge::openjdk=8.0.144 # Don't upgrade - required for GATK
   - bioconda::fastqc=0.11.9
@@ -26,7 +26,7 @@ dependencies:
   - bioconda::qualimap=2.2.2d
   - bioconda::vcf2genome=0.91
   - bioconda::damageprofiler=0.4.9 # Don't upgrade - later versions don't allow java 8
-  - bioconda::multiqc=1.13
+  - bioconda::multiqc=1.14
   - bioconda::pmdtools=0.60
   - bioconda::bedtools=2.30.0
   - conda-forge::libiconv=1.16

nextflow.config

@@ -285,7 +285,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/eager:2.4.6'
+process.container = 'nfcore/eager:2.4.7'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -415,7 +415,7 @@ manifest {
   description = 'A fully reproducible and state-of-the-art ancient DNA analysis pipeline'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.07.1'
-  version = '2.4.6'
+  version = '2.4.7'
 }
 
 // Function to ensure that resource requirements don't go beyond