Merge pull request #34 from uclahs-cds/jsalmingo-update-picard-to-311

Update Picard version to 3.1.1

CHANGELOG.md

@@ -7,6 +7,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.1.1] - 2023-11-15
+### Added
+ - Update Picard 3.1.1
+
 ## [3.1.0] - 2023-09-19
 ### Added
  - Update Picard 3.1.0

Dockerfile

@@ -2,7 +2,7 @@ ARG MINIFORGE_VER=23.3.1-1
 FROM condaforge/mambaforge:${MINIFORGE_VER} AS builder
 
 # Use mamba to install tools and dependencies into /usr/local
-ARG PICARD_VERSION=3.1.0
+ARG PICARD_VERSION=3.1.1
 RUN mamba create -qy -p /usr/local \
     -c bioconda \
     -c conda-forge \

README.md

@@ -4,12 +4,12 @@ UCLA CDS Dockerfile for Picard (picard-slim) from the Broad Institute. A set of
 # Documentation
 
 Picard can be found on GitHub at [broadinstitute/picard](https://github.com/broadinstitute/picard).
-`picard.jar` can be found at `/usr/local/share/picard-slim-3.1.0-0/picard.jar`
+`picard.jar` can be found at `/usr/local/share/picard-slim-3.1.1-0/picard.jar`
 
 # Version
 | Tool | Version |
 |------|---------|
-| picard-slim | 3.1.0 |
+| picard-slim | 3.1.1 |
 | Java | 1.17 |
 
 ## References

metadata.yaml

@@ -5,7 +5,7 @@ Maintainers: ['[email protected]']
 Contributors: ['Aaron Holmes', 'Helena Winata', 'Jieun Oh', 'Takafumi Yamaguchi', 'Arpi Beshlikyan', 'Selina Wu', 'Beth Neilsen', 'Joseph Salmingo']
 Languages: ['Dockerfile']
 Tools: ['Picard']
-Version: ['3.1.0']
+Version: ['3.1.1']
 Purpose: 'A set of tools for manipulating SAM/BAM/CRAM and VCF file formats'
 References: 'https://github.com/broadinstitute/picard'
 image_name: 'picard'