Release 4.0.1 (#85)

* Update metadata.yaml * Update nextflow.config * Update CHANGELOG.md * Update README.md * update GH registry in CICD base * Update CHANGELOG.md Co-authored-by: Mootor <mmootor@ip-0A125238.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>
uclahs-cds · Dec 12, 2022 · 74a2ae2 · 74a2ae2
1 parent 6ef3c28
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diff --git a/.github/workflows/cicd-base.yaml b/.github/workflows/cicd-base.yaml
@@ -22,4 +22,4 @@ jobs:
 
       # Run CICD-base
       - name: CICD-base
-        uses: docker://blcdsdockerregistry/cicd-base:latest
+        uses: docker://ghcr.io/uclahs-cds/cicd-base:latest
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,10 @@ All notable changes to the call-gSV pipeline.
 ---
 
 ## [Unreleased]
+
+---
+
+## [4.0.1] - 2022-12-12
 ### Changed
 - Parameterize Docker registry
 - Use `ghcr.io/uclahs-cds` as default registry

diff --git a/README.md b/README.md
@@ -280,7 +280,7 @@ Note, per Nature the following benchmarks exist for the human genome:
 
 ### Validation Tool
 
-Included is a template for validating your input files. For more information on the tool check out: https://github.com/uclahs-cds/tool-validate-nf
+Included is a template for validating your input files. For more information on the tool check out: https://github.com/uclahs-cds/public-tool-PipeVal
 
 ---
 

diff --git a/metadata.yaml b/metadata.yaml
@@ -5,4 +5,4 @@ maintainers: "Boutros Lab Infrastructure [email protected]
 languages: ["Nextflow", "Docker"]
 dependencies: ["Java", "Nextflow", "Docker"]
 references: "https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Guide+to+Nextflow"
-tools: ["Delly:v1.1.3", "Manta:v1.6.0", "BCFtools:v1.15.1", "VCFtools:v0.1.16", "RTG-tools:v3.12", "Validate-nf:v2.1.5"]
+tools: ["Delly:v1.1.3", "Manta:v1.6.0", "BCFtools:v1.15.1", "VCFtools:v0.1.16", "RTG-tools:v3.12", "PipeVal:v3.0.0"]
diff --git a/nextflow.config b/nextflow.config
@@ -4,5 +4,5 @@ manifest {
     name = 'call-gSV'
     author = 'Yu Pan, Tim Sanders, Yael Berkovich, Mohammed Faizal Eeman Mootor'
     description = 'A pipeline to call germline structural variants utilizing Delly and Manta'
-    version = '4.0.0'
+    version = '4.0.1'
 }
-Original file line number
+Diff line change
@@ Expand Up @@
     ### Validation Tool
-    Included is a template for validating your input files. For more information on the tool check out: https://github.com/uclahs-cds/tool-validate-nf
+    Included is a template for validating your input files. For more information on the tool check out: https://github.com/uclahs-cds/public-tool-PipeVal
     ---
@@ Expand Down @@