Update Delly 1.1.5 (#12)

* closes #11 - update Delly to v1.1.5

* Update CHANGELOG.md

* Update metadata.yaml

* Update README.md

* Add Docker-build-release.yaml

* Update .gitignore

* change Image_name to image_name in Docker-build-release.yaml

* Update README.md

* Update CHANGELOG.md

* Update Docker-build-release.yaml

* fix yaml linting in Docker-build-release.yaml

Co-authored-by: Mootor <mmootor@ip-0A12521C.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>

.github/workflows/Docker-build-release.yaml

@@ -0,0 +1,20 @@
+---
+on:
+  push:
+    branches: ['main']
+    tags: ['v*']
+  release:
+    types: [published]
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    name: A job to build and push a docker image
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - id: build-push
+        uses: uclahs-cds/tool-Docker-action/build-release@latest
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -1,8 +1,81 @@
 # System files
+*.log
 .DS_Store
 
 # R
 .Rhistory
 .Rapp.history
 .Rproj.user
-.RData
+*.RData
+*.rd[as]
+
+# Python
+__pycache__/
+.pytest_cache/
+.Python
+pip-log.txt
+pip-delete-this-directory.txt
+*.py[cod]
+*$py.class
+venv
+.venv
+.env
+
+# VScode
+.vscode
+
+# Nextflow
+work/
+.nextflow/
+*.nextflow.log*
+
+## Molecular files
+
+# Array file
+*.CEL
+*.cel
+*.OSCHP
+
+# Sequence file (e.g. Reference genome)
+*.fasta
+*.fa
+*.fai
+*.dict
+*.gtf
+
+# FASTQ file
+*.fq
+*.fastq
+
+# Proteomics file
+*.raw
+*.mzML
+*.mzXML
+*.mgf
+*.idXML
+*.consensusXML
+*.featureXML
+*.mzid
+*.mzData
+*.dta
+*.dta2d
+
+# DNA/RNA alignment file
+*.sam
+*.bam
+*.bai
+*.cram
+*.crai
+
+# Variant file
+*.bcf
+*.csi
+*.vcf
+*.tbi
+*.maf
+
+# Compressed file
+*.gz
+*.tar
+*.zip
+

CHANGELOG.md

@@ -11,6 +11,16 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ---
 
+## [1.1.5] - 2022-10-24
+### Added
+- Add `Docker-build-release.yaml` to the repo
+
+### Changed
+- Update Delly v1.1.5 in Dockerfile
+- Update `.gitignore` file
+
+---
+
 ## [1.1.3] - 2022-08-03
 ### Changed
 - Replace `conda` with `mamba` in Dockerfile based on the BL Docker Template

Dockerfile

@@ -1,7 +1,7 @@
 FROM blcdsdockerregistry/bl-base:1.1.0 AS builder
 
 # Use conda to install tools and dependencies into /usr/local
-ARG DELLY_VERSION=1.1.3
+ARG DELLY_VERSION=1.1.5
 RUN mamba create -qy -p /usr/local \
     -c bioconda \
     -c conda-forge \

README.md

@@ -1,7 +1,7 @@
-# docker-delly
+# docker-Delly
 Repository for the Boutros Lab Delly Dockerfile, "an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data."
 
-The image is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/delly
+This image can be found in docker-Delly's GitHub package page [here](https://github.com/uclahs-cds/docker-Delly/pkgs/container/delly).
 
 # Documentation
 Delly GitHub repository [here](https://github.com/dellytools/delly)
@@ -10,7 +10,7 @@ Delly GitHub repository [here](https://github.com/dellytools/delly)
 # Version
 | Tool | Version |
 |------|---------|
-|Delly| 1.1.3|
+|Delly| 1.1.5|
 
 
 ---
@@ -28,9 +28,9 @@ https://doi.org/10.1093/bioinformatics/bts378
 
 Author: 'Timothy Sanders', 'Yu Pan', 'Mohammed Faizal Eeman Mootor'
 
-docker-delly is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
+docker-Delly is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
 
-docker-delly can be used to create a docker instance to use the Delly tool. 
+docker-Delly can be used to create a docker instance to use the Delly tool. 
 
 Copyright (C) 2021-2022 University of California Los Angeles ("Boutros Lab") All rights reserved.
 

metadata.yaml

@@ -1,10 +1,10 @@
 ---
-Category: 'docker'
-Description: 'Docker repository for Delly'
-Maintainers: ['[email protected]', '[email protected]']
-Contributors: ['Timothy Sanders', 'Yu Pan', 'Mohammed Faizal Eeman Mootor']
-Languages: ['Dockerfile']
-Tools: ['Delly']
-Version: ['1.1.3']
-Purpose of tool: 'Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.'
-References: 'https://github.com/dellytools/delly'
+category: 'docker'
+description: 'Docker repository for Delly'
+maintainers: ['[email protected]', '[email protected]']
+languages: ['Dockerfile']
+tools: ['Delly']
+version: ['1.1.5']
+purpose: 'Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.'
+references: 'https://github.com/dellytools/delly'
+image_name: 'delly'