Release v6.0.0 (#221)

* Update call-gSV version * Update version to v6.0.0 * Update CHANGELOG * Update metadata * Update author list
uclahs-cds · Jul 11, 2024 · 58df3e1 · 58df3e1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,12 +8,16 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+
+---
+
+## [6.0.0] - 2024-07-10
 ### Changed
 + Call-SRC: `2.0.0-rc.1` -> `2.0.0`
 + Align-DNA: `10.0.0` -> `10.1.0`
 + Recalibrate-BAM: `1.0.0` -> `1.0.1`
 + Call-sSNV: `8.0.0` -> `8.1.0`
-+ Call-gSV: `5.0.0` -> `5.1.0`
++ Call-gSV: `5.0.0` -> `5.2.0`
 + Call-sCNA: `3.1.0` -> `3.2.0`
 ### Fixed
 + Issue with empty email addresses resulting in argument errors

diff --git a/external/pipeline-call-gSV b/external/pipeline-call-gSV
diff --git a/metadata.yaml b/metadata.yaml
@@ -1,6 +1,6 @@
 ---
 Category: "pipeline"
-Description: "Nextflow pipeline to convert BAM to FASTQ, align, call gSNP, call sSNV, and call mtSNV"
+Description: "Nextflow pipeline to convert BAM to FASTQ, align, perform QC, assess targeted coverage, call gSNP, call sSNV, call mtSNV, call SVs, call sCNA, and perform subclonal reconstruction"
 Maintainers: "Chenghao Zhu <[email protected]>, Yash Patel <[email protected]>, Nicholas Wang <[email protected]>, Helena Winata <[email protected]>, Mohammed Faizal Eeman Mootor <[email protected]>"
 Languages: ["Nextflow"]
 Dependencies: ["Java", "Nextflow", "Docker"]

diff --git a/nextflow.config b/nextflow.config
@@ -1,7 +1,7 @@
 // Metadata
 manifest {
     name = 'metapipeline-DNA'
-    author = ['Yash Patel', 'Chenghao Zhu', 'Helena Winata', 'Alfredo Enrique Gonzalez', 'Nicholas Wang', 'Sorel Fitz-Gibbon', 'Mohammed Faizal Eeman Mootor', 'Nicole Zeltser']
-    description = 'Nextflow pipeline to convert BAM to FASTQ, align, call gSNP, call sSNV, call gSV, call sSV and call mtSNV'
-    version = '6.0.0-rc.6'
+    author = ['Yash Patel', 'Chenghao Zhu', 'Helena Winata', 'Alfredo Enrique Gonzalez', 'Nicholas Wang', 'Sorel Fitz-Gibbon', 'Mohammed Faizal Eeman Mootor', 'Nicole Zeltser', 'Nicholas Wiltsie', 'Takafumi Yamaguchi']
+    description = 'Nextflow pipeline to convert BAM to FASTQ, align, perform QC, assess targeted coverage, call gSNP, call sSNV, call mtSNV, call SVs, call sCNA, and perform subclonal reconstruction'
+    version = '6.0.0'
 }
+9 −2		.github/dependabot.yml
+10 −0		CHANGELOG.md
+52 −4		README.md
+1 −1		config/F16.config
+1 −1		config/F32.config
+1 −1		config/F72.config
+1 −1		config/M64.config
+65 −3		config/custom_schema_types.config
+15 −0		config/methods.config
+13 −0		config/schema.yaml
+2 −0		config/template.config
+1 −1		external/pipeline-Nextflow-config
+1 −1		external/pipeline-Nextflow-module
+0 −6		module/bcftools.nf
+0 −24		module/delly.nf
+1 −7		module/manta.nf
+0 −6		module/rtgtools.nf
+1 −5		module/sha512.nf
+0 −6		module/vcftools.nf
+1 −1		nextflow.config
+20 −0		nftest.yaml
+46 −0		test/config/base-resource-update.config
+37 −8		test/configtest-F16.json