Merge pull request #15 from uclahs-cds/yupan-use-docker-delly-0.9.1

Upgade delly version from 0.8.7 to 0.9.1
uclahs-cds · Dec 18, 2021 · 72af52b · 72af52b
2 parents 403c980 + 7c8111d
commit 72af52b
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Showing 5 changed files with 9 additions and 7 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,15 +7,17 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ---
 
-## [Unreleased]
+## [1.0.1] - 2021-12-09
+### Changed
+- Change Delly version from 0.8.7 to 0.9.1 in nextflow.config and metadata.yaml
 
 ---
 
-## [1.0.0] - 2020-10-29
+## [1.0.0] - 2021-10-29
 ### Changed
 - Minor changes of wording in CHANGELOG.md and metadata.yaml
 
-## [1.0.0-rc1] - 2020-10-18
+## [1.0.0-rc1] - 2021-10-18
 ### Added
 - Use Delly to call the somatic structural variants (SVs) of one tumor sample and a matched control sample, further filter the somatic SVs.
 - Add option to specify `map_qual`, `min_clique_size`, and `mad_cutoff` Delly filters to reduce the runtime.

diff --git a/metadata.yaml b/metadata.yaml
@@ -6,6 +6,6 @@ Contributors: ["Yu Pan", "Ghouse Mohammed"]
 Languages: ["Nextflow", "Docker"]
 Dependencies: ["Java", "Nextflow", "Docker"]
 References: "https://uclahs.box.com/s/qfzr99sc8ntmfddn30ii62wx4273utoz"
-Tools: ["Delly:v0.8.7", "BCFtools:v1.12", "PipeVal:v2.1.5"]
+Tools: ["Delly:v0.9.1", "BCFtools:v1.12", "PipeVal:v2.1.5"]
 Engineering_Owner: ["Yu Pan"]
 Scientific_Owner: ["Takafumi Yamaguchi"]
diff --git a/pipeline/config/methods.config b/pipeline/config/methods.config
@@ -7,7 +7,7 @@ manifest {
     author = "Yu Pan, Ghouse Mohammed"
     homePage = "https://github.com/uclahs-cds/pipeline-call-sSV"
     description = "A pipeline to call somatic SVs utilizing Delly"
-    version = "1.0.0"
+    version = "1.0.1"
     }
 
 methods {

diff --git a/pipeline/config/nextflow.config b/pipeline/config/nextflow.config
@@ -17,7 +17,7 @@ params {
     cache_intermediate_pipeline_steps = false
 
     // Pipeline tool versions
-    delly_version = '0.8.7'
+    delly_version = '0.9.1'
     bcftools_version = '1.12'
     validate_version = '2.1.5'
 

diff --git a/pipeline/modules/sha512.nf b/pipeline/modules/sha512.nf
@@ -30,6 +30,6 @@ process generate_sha512 {
     script:
         """
         set -euo pipefail
-        python -m validate -t sha512-gen $input_checksum_file > ${input_checksum_file}.sha512
+        sha512sum $input_checksum_file > ${input_checksum_file}.sha512
         """
     }