From 6022291e06aaeb40cf9e0ef0d187c62ffac8c1c1 Mon Sep 17 00:00:00 2001 From: ryanjameskennedy Date: Fri, 23 Feb 2024 12:00:30 +0100 Subject: [PATCH] Update v0.4.0 to v0.5.0 --- CHANGELOG.md | 8 + configs/nextflow.base.config | 4 +- configs/nextflow.ci.config | 4 +- configs/nextflow.hopper.config | 2 +- configs/nextflow.ngp.config | 4 +- configs/nextflow.selftest.config | 4 +- deploy/reqs/env-index-mini.yaml | 8 - deploy/reqs/env-index.yaml | 38 ---- deploy/reqs/freeze.txt | 300 ------------------------------- 9 files changed, 17 insertions(+), 355 deletions(-) delete mode 100644 deploy/reqs/env-index-mini.yaml delete mode 100644 deploy/reqs/env-index.yaml delete mode 100644 deploy/reqs/freeze.txt diff --git a/CHANGELOG.md b/CHANGELOG.md index 7fc5d3eb..990a2c94 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added +### Fixed + +### Changed + +## [0.5.0] + +### Added + - Added a GitHub workflow to run a basic CI pipeline. - Build prp as singularity image from dockerhub in Makefile - Chewbacca and virulencefinder sif fetched from galaxyproject diff --git a/configs/nextflow.base.config b/configs/nextflow.base.config index eb06f09b..a6180298 100644 --- a/configs/nextflow.base.config +++ b/configs/nextflow.base.config @@ -253,8 +253,8 @@ dag { } manifest { - homePage = 'https://github.com/genomic-medicine-sweden/JASEN' + homePage = 'https://github.com/genomic-medicine-sweden/jasen' description = 'Pipeline epitypes numerous bacterial species as well as identifies AMR and virulence genes' mainScript = 'main.nf' - version = '0.4.0' + version = '0.5.0' } diff --git a/configs/nextflow.ci.config b/configs/nextflow.ci.config index 05d8bae3..d8caad9e 100644 --- a/configs/nextflow.ci.config +++ b/configs/nextflow.ci.config @@ -253,8 +253,8 @@ singularity { } manifest { - homePage = 'https://github.com/genomic-medicine-sweden/JASEN' + homePage = 'https://github.com/genomic-medicine-sweden/jasen' description = 'Pipeline epitypes numerous bacterial species as well as identifies AMR and virulence genes' mainScript = 'main.nf' - version = '0.4.0' + version = '0.5.0' } diff --git a/configs/nextflow.hopper.config b/configs/nextflow.hopper.config index 69fe5210..72d8f7f9 100644 --- a/configs/nextflow.hopper.config +++ b/configs/nextflow.hopper.config @@ -253,5 +253,5 @@ manifest { homePage = 'https://github.com/genomic-medicine-sweden/jasen' description = 'Pipeline epitypes numerous bacterial species as well as identifies AMR and virulence genes' mainScript = 'main.nf' - version = '0.4.0' + version = '0.5.0' } diff --git a/configs/nextflow.ngp.config b/configs/nextflow.ngp.config index 38e30a02..cb44f6c0 100644 --- a/configs/nextflow.ngp.config +++ b/configs/nextflow.ngp.config @@ -254,8 +254,8 @@ process { } manifest { - homePage = 'https://github.com/genomic-medicine-sweden/JASEN' + homePage = 'https://github.com/genomic-medicine-sweden/jasen' description = 'Pipeline epitypes numerous bacterial species as well as identifies AMR and virulence genes' mainScript = 'main.nf' - version = '0.4.0' + version = '0.5.0' } diff --git a/configs/nextflow.selftest.config b/configs/nextflow.selftest.config index bc9a7c2e..3e476fe0 100644 --- a/configs/nextflow.selftest.config +++ b/configs/nextflow.selftest.config @@ -253,8 +253,8 @@ process { } manifest { - homePage = 'https://github.com/genomic-medicine-sweden/JASEN' + homePage = 'https://github.com/genomic-medicine-sweden/jasen' description = 'Pipeline epitypes numerous bacterial species as well as identifies AMR and virulence genes' mainScript = 'main.nf' - version = '0.4.0' + version = '0.5.0' } diff --git a/deploy/reqs/env-index-mini.yaml b/deploy/reqs/env-index-mini.yaml deleted file mode 100644 index a9fe4738..00000000 --- a/deploy/reqs/env-index-mini.yaml +++ /dev/null @@ -1,8 +0,0 @@ -name: jasen -channels: - - conda-forge - - bioconda -dependencies: - - bwa - - blast - - chewbbaca diff --git a/deploy/reqs/env-index.yaml b/deploy/reqs/env-index.yaml deleted file mode 100644 index 8ee64654..00000000 --- a/deploy/reqs/env-index.yaml +++ /dev/null @@ -1,38 +0,0 @@ -name: jasen -channels: - - anaconda - - bioconda - - conda-forge - - defaults -dependencies: - - openjdk - - python=3.7.1 - - bcftools=1.5 - - blast - - bowtie2 - - bwa - - cd-hit - - cgecore - - chewbbaca - - fastqc - - freebayes - - gatk4 - - gitpython - - libiconv - - kraken2 - - mlst - - picard - - pip - - pymummer - - pysam - - quast - - r-base - - samtools - - spades - - tabulate - - trimmomatic - - vcftools - - pip: - - biopython - - pandas - - multiqc diff --git a/deploy/reqs/freeze.txt b/deploy/reqs/freeze.txt deleted file mode 100644 index c403f34b..00000000 --- a/deploy/reqs/freeze.txt +++ /dev/null @@ -1,300 +0,0 @@ -# This file may be used to create an environment using: -# $ conda create --name --file -# platform: linux-64 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