Update Picard to 3.0.0 (#24)

Co-authored-by: Neilsen <bneilsen@ip-0A12524C.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>
uclahs-cds · Mar 7, 2023 · 5d16bec · 5d16bec
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## ## [Unreleased]
 
+## [3.0.0] - 2023-03-03
+### Added
+- Update Picard 3.0.0
+
 ## [2.27.4] - 2022-08-03
 ### Added
 - Update Picard to 2.27.4

diff --git a/Dockerfile b/Dockerfile
@@ -1,9 +1,10 @@
 FROM blcdsdockerregistry/bl-base:1.1.0 AS builder
 
 # Use mamba to install tools and dependencies into /usr/local
-ARG PICARD_VERSION=2.27.4
+ARG PICARD_VERSION=3.0.0
 RUN mamba create -qy -p /usr/local \
     -c bioconda \
+    -c conda-forge \
     picard-slim==${PICARD_VERSION}
 
 # Deploy the target tools into a base image

diff --git a/README.md b/README.md
@@ -4,13 +4,13 @@ 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-2.27.4-0/picard.jar`
+`picard.jar` can be found at `/usr/local/share/picard-slim-3.0.0/picard.jar`
 
 # Version
 | Tool | Version |
 |------|---------|
-| picard-slim | 2.27.4 |
-| Java | 1.8 |
+| picard-slim | 3.0.0 |
+| Java | 1.17 |
 
 ## References
 

diff --git a/metadata.yaml b/metadata.yaml
@@ -2,9 +2,9 @@
 Category: 'docker'
 Description: 'Docker repository for Picard'
 Maintainers: ['selinawu@mednet.ucla.edu']
-Contributors: ['Aaron Holmes', 'Helena Winata', 'Jieun Oh', 'Takafumi Yamaguchi', 'Arpi Beshlikyan', 'Selina Wu']
+Contributors: ['Aaron Holmes', 'Helena Winata', 'Jieun Oh', 'Takafumi Yamaguchi', 'Arpi Beshlikyan', 'Selina Wu', 'Beth Neilsen']
 Languages: ['Dockerfile']
 Tools: ['Picard']
-Version: ['2.27.4']
+Version: ['3.0.0']
 Purpose: 'A set of tools for manipulating SAM/BAM/CRAM and VCF file formats'
 References: 'https://github.com/broadinstitute/picard'