From becd25667cf0206269011a8c6b8a38229851de64 Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Tue, 30 Nov 2021 09:21:39 +0100 Subject: [PATCH 1/2] Verision bump 2.4.1 --- .github/workflows/ci.yml | 4 ++-- CHANGELOG.md | 4 ++-- Dockerfile | 4 ++-- environment.yml | 2 +- nextflow.config | 4 ++-- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 21b7ae020..70e0ec0ac 100644 --- a/.github/workflows/ci.yml +++ b/.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:dev + run: docker build --no-cache . -t nfcore/eager:2.4.1 - name: Pull docker image if: ${{ !env.MATCHED_FILES }} run: | docker pull nfcore/eager:dev - docker tag nfcore/eager:dev nfcore/eager:dev + docker tag nfcore/eager:dev nfcore/eager:2.4.1 - name: Install Nextflow env: diff --git a/CHANGELOG.md b/CHANGELOG.md index 595c0132a..033f389de 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). -## 2.4.1[dev] +## [2.4.1] - 2021-11-30 ### `Added` @@ -21,7 +21,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Deprecated` -## [2.4.0] - Wangen - 20201-09-14 +## [2.4.0] - Wangen - 2021-09-14 ### `Added` diff --git a/Dockerfile b/Dockerfile index 7087c402a..1354408d3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,7 +7,7 @@ COPY environment.yml / RUN conda env create --quiet -f /environment.yml && conda clean -a # Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-eager-2.4.1dev/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-eager-2.4.1/bin:$PATH # Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-eager-2.4.1dev > nf-core-eager-2.4.1dev.yml \ No newline at end of file +RUN conda env export --name nf-core-eager-2.4.1 > nf-core-eager-2.4.1.yml \ No newline at end of file diff --git a/environment.yml b/environment.yml index 3b007e300..db6c11b10 100644 --- a/environment.yml +++ b/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-2.4.1dev +name: nf-core-eager-2.4.1 channels: - conda-forge - bioconda diff --git a/nextflow.config b/nextflow.config index 2ca068747..20076e27e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -284,7 +284,7 @@ params { // Container slug. Stable releases should specify release tag! // Developmental code should specify :dev -process.container = 'nfcore/eager:dev' +process.container = 'nfcore/eager:2.4.1' // Load base.config by default for all pipelines includeConfig 'conf/base.config' @@ -414,7 +414,7 @@ manifest { description = 'A fully reproducible and state-of-the-art ancient DNA analysis pipeline' mainScript = 'main.nf' nextflowVersion = '>=20.07.1' - version = '2.4.1dev' + version = '2.4.1' } // Function to ensure that resource requirements don't go beyond From d2f4be4eab7e823759b73771228b481b2cf092fa Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Tue, 30 Nov 2021 09:36:55 +0100 Subject: [PATCH 2/2] Added mentions --- CHANGELOG.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 033f389de..31d4adf35 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,15 +7,15 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Added` -- [#805](https://github.com/nf-core/eager/issues/805) Changes to bam_trim options to allow flexible trimming by library strandedness (in addition to UDG treatment). -- [#808](https://github.com/nf-core/eager/issues/808) Retain read group information across bam merges. Sample set to sample name (rather than library name) in bwa output 'RG' readgroup tag. -- Map and base quality filters prior to genotyping with pileupcaller can now be specified. -- [#774](https://github.com/nf-core/eager/issues/774) Added support for multi-threaded Bowtie2 build reference genome indexing -- [#804](https://github.com/nf-core/eager/issues/804) Improved output documentation description to add how 'cluster factor' is calculated +- [#805](https://github.com/nf-core/eager/issues/805) Changes to bam_trim options to allow flexible trimming by library strandedness (in addition to UDG treatment). (@TCLamnidis) +- [#808](https://github.com/nf-core/eager/issues/808) Retain read group information across bam merges. Sample set to sample name (rather than library name) in bwa output 'RG' readgroup tag. (@TCLamnidis) +- Map and base quality filters prior to genotyping with pileupcaller can now be specified. (@TCLamnidis) +- [#774](https://github.com/nf-core/eager/issues/774) Added support for multi-threaded Bowtie2 build reference genome indexing (@jfy133) +- [#804](https://github.com/nf-core/eager/issues/804) Improved output documentation description to add how 'cluster factor' is calculated (thanks to @meganemichel) ### `Fixed` -- [#803](https://github.com/nf-core/eager/issues/803) Fixed mistake in metro-map diagram (`samtools index` is now correctly `samtools faidx`) +- [#803](https://github.com/nf-core/eager/issues/803) Fixed mistake in metro-map diagram (`samtools index` is now correctly `samtools faidx`) (@jfy133) ### `Dependencies`