Merge branch 'major-release-wangen' into inline-barcode-trimming

Author: jfy133

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Added`
 
 - [#642](https://github.com/nf-core/eager/issues/642) and [#431](https://github.com/nf-core/eager/issues/431) adds post-adapter removal barcode/fastq trimming
+
 ### `Fixed`
 
 - [#771](https://github.com/nf-core/eager/issues/771) Remove legacy code
@@ -16,20 +17,26 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Dependencies`
 
 ### `Deprecated`
-## v2.3.5dev - [date]
+
+## v2.3.5 - 2021-06-03
 
 ### `Added`
 
 - [#722](https://github.com/nf-core/eager/issues/722) - Adds bwa `-o` flag for more flexibility in bwa parameters
 - [#736](https://github.com/nf-core/eager/issues/736) - Add printing of multiqc run report location on successful completion
+- New logo that is more visible when a user is using darkmode on GitHub or nf-core website!
 
 ### `Fixed`
 
 - [#723](https://github.com/nf-core/eager/issues/723) - Fixes empty fields in TSV resulting in uninformative error
 - Updated template to nf-core/tools 1.14
 - [#688](https://github.com/nf-core/eager/issues/688) - Clarified the pipeline is not just for humans and microbes, but also plants and animals, and also for modern DNA
 - [#751](https://github.com/nf-core/eager/pull/751) - Added missing label to mtnucratio
-- General code cleanup and standarisation of parameters with no default setting
+- General code cleanup and standardisation of parameters with no default setting
+- [#750](https://github.com/nf-core/eager/issues/750) - Fixed piped commands requesting the same number of CPUs at each command step
+- [#757](https://github.com/nf-core/eager/issues/757) - Removed confusing 'Data Type' variable from MultiQC workflow summary (not consistent with TSV input)
+- [#759](https://github.com/nf-core/eager/pull/759) - Fixed malformed software scraping regex that resulted in N/A in MultiQC report
+- [#761](https://github.com/nf-core/eager/pull/759) - Fixed issues related to instability of samtools filtering related CI tests
 
 ### `Dependencies`
 

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-2.3.5dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.4dev/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.3.5dev > nf-core-eager-2.3.5dev.yml
+RUN conda env export --name nf-core-eager-2.4dev > nf-core-eager-2.4dev.yml

README.md

@@ -1,4 +1,4 @@
-# ![nf-core/eager](docs/images/nf-core_eager_logo.png)
+# ![nf-core/eager](docs/images/nf-core_eager_logo_outline_drop.png)
 
 **A fully reproducible and state-of-the-art ancient DNA analysis pipeline**.
 
@@ -7,6 +7,7 @@
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.07.1-brightgreen.svg)](https://www.nextflow.io/)
 [![nf-core](https://img.shields.io/badge/nf--core-pipeline-brightgreen.svg)](https://nf-co.re/)
 [![DOI](https://zenodo.org/badge/135918251.svg)](https://zenodo.org/badge/latestdoi/135918251)
+[![Published in PeerJ](https://img.shields.io/badge/peerj-published-%2300B2FF)](https://peerj.com/articles/10947/)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
 [![Docker](https://img.shields.io/docker/automated/nfcore/eager.svg)](https://hub.docker.com/r/nfcore/eager)

assets/multiqc_config.yaml

@@ -1,4 +1,4 @@
-custom_logo: 'nf-core_eager_logo.png'
+custom_logo: 'nf-core_eager_logo_outline_drop.png'
 custom_logo_url: https://github.com/nf-core/eager/
 custom_logo_title: 'nf-core/eager'
 

bin/scrape_software_versions.py

@@ -16,7 +16,7 @@
     'Bowtie2': ['v_bowtie2.txt', r"bowtie2-([0-9]+\.[0-9]+\.[0-9]+) -fdebug"],
     'Qualimap': ['v_qualimap.txt', r"QualiMap v.(\S+)"],
     'GATK HaplotypeCaller': ['v_gatk.txt', r" v(\S+)"],
-    #'GATK UnifiedGenotyper': ['v_gatk3_5.txt', r"version (\S+)"],
+    'GATK UnifiedGenotyper': ['v_gatk3.txt', r"(\S+)"],
     'bamUtil' : ['v_bamutil.txt', r"Version: (\S+);"],
     'fastP': ['v_fastp.txt', r"([\d\.]+)"],
     'DamageProfiler' : ['v_damageprofiler.txt', r"DamageProfiler v(\S+)"],
@@ -37,7 +37,7 @@
     'kraken':['v_kraken.txt', r"Kraken version (\S+)"],
     'eigenstrat_snp_coverage':['v_eigenstrat_snp_coverage.txt',r"(\S+)"],
     'mapDamage2':['v_mapdamage.txt',r"(\S+)"],
-    'bbduk':['v_bbduk.txt',r"(\S+)"]
+    'bbduk':['v_bbduk.txt',r"(.*)"]
 }
 
 results = OrderedDict()