Merge pull request #763 from nf-core/dev

Release PR for 2.3.5 patch

Author: jfy133

.github/PULL_REQUEST_TEMPLATE.md

@@ -10,14 +10,15 @@ Remember that PRs should be made against the dev branch, unless you're preparing
 
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
 -->
+<!-- markdownlint-disable ul-indent -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-  - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
-  - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
-  - [ ] If necessary, also make a PR on the nf-core/eager _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+    - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
+    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](<https://github.com/>nf-core/eager/tree/master/.github/CONTRIBUTING.md)
+    - [ ] If necessary, also make a PR on the nf-core/eager _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint .`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/ci.yml

@@ -8,6 +8,9 @@ on:
   release:
     types: [published]
 
+# Uncomment if we need an edge release of Nextflow again
+# env: NXF_EDGE: 1
+
 jobs:
   test:
     name: Run workflow tests
@@ -20,7 +23,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['20.07.1', '21.03.0-edge']
+        nxf_ver: ['20.07.1', '']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -34,13 +37,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/eager:2.3.4
+        run: docker build --no-cache . -t nfcore/eager:2.3.5
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:2.3.4
+          docker tag nfcore/eager:dev nfcore/eager:2.3.5
 
       - name: Install Nextflow
         env:

CHANGELOG.md

@@ -3,16 +3,40 @@
 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).
 
+## 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 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`
+
+### `Deprecated`
+
 ## v2.3.4 - 2021-05-05
 
 ### `Added`
 
-- [#729](https://github.com/nf-core/eager/issues/729) Added Bowtie2 flag `--maxins` for PE mapping modern DNA mapping contexts
+- [#729](https://github.com/nf-core/eager/issues/729) - Added Bowtie2 flag `--maxins` for PE mapping modern DNA mapping contexts
 
 ### `Fixed`
 
 - Corrected explanation of the "--min_adap_overlap" parameter for AdapterRemoval in the docs
-- [#725](https://github.com/nf-core/eager/pull/725) `bwa_index` doc update
+- [#725](https://github.com/nf-core/eager/pull/725) - `bwa_index` doc update
 - Re-adds gzip piping to AdapterRemovalFixPrefix to speed up process after reports of being very slow
 - Updated DamageProfiler citation from bioRxiv to publication
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM nfcore/base:1.13.3
+FROM nfcore/base:1.14
 LABEL authors="The nf-core/eager community" \
       description="Docker image containing all software requirements for the nf-core/eager pipeline"
 
@@ -7,11 +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-2.3.4/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.3.5/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.3.4 > nf-core-eager-2.3.4.yml
-
-# Instruct R processes to use these empty files instead of clashing with a local version
-RUN touch .Rprofile
-RUN touch .Renviron
+RUN conda env export --name nf-core-eager-2.3.5 > nf-core-eager-2.3.5.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**.
 
@@ -17,7 +17,7 @@
 ## Introduction
 
 <!-- nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
-**nf-core/eager** is a bioinformatics best-practise analysis pipeline for NGS sequencing based ancient DNA (aDNA) data analysis.
+**nf-core/eager** is a scalable and reproducible bioinformatics best-practise processing pipeline for genomic NGS sequencing data, with a focus on ancient DNA (aDNA) data. It is ideal for the (palaeo)genomic analysis of humans, animals, plants, microbes and even microbiomes.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. The pipeline pre-processes raw data from FASTQ inputs, or preprocessed BAM inputs. It can align reads and performs extensive general NGS and aDNA specific quality-control on the results. It comes with docker, singularity or conda containers making installation trivial and results highly reproducible.
 
@@ -27,7 +27,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 ## Quick Start
 
-1. Install [`nextflow`](https://nf-co.re/usage/installation) (version >= 20.04.0)
+1. Install [`nextflow`](https://nf-co.re/usage/installation) (`>=20.07.1`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
 

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()