Merge pull request #24 from uclahs-cds/ts-docker-updates

Docker repo updates
uclahs-cds · May 8, 2021 · 41e86bd · 41e86bd
2 parents e8aed01 + 977f863
commit 41e86bd
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diff --git a/.github/workflows/cicd-base.yaml b/.github/workflows/cicd-base.yaml
@@ -4,10 +4,10 @@ name: CICD-base
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
 
 jobs:
   CICD-base:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,12 @@
 # Changelog
 All notable changes to the call-gSV pipeline.
 
+## [2.2.0] - 2021-05-07
+### Changed
+- Updated modules to point to tool specific Docker Hub repos
+- Update of BCFtools from 1.11 to 1.12
+- Update of RTG-tools from 3.11 to 3.12
+
 ## [2.1.0] - 2021-04-01
 ### Added
 - Added Validate-nf logging outputs to output logging directory

diff --git a/docker/bcftools/Dockerfile b/docker/bcftools/Dockerfile
diff --git a/docker/delly/Dockerfile b/docker/delly/Dockerfile
diff --git a/docker/rtgtools/Dockerfile b/docker/rtgtools/Dockerfile
diff --git a/docker/vcftools/Dockerfile b/docker/vcftools/Dockerfile
diff --git a/metadata.yaml b/metadata.yaml
@@ -4,8 +4,8 @@ Description: "a pipeline for calling structural variants and copy number variant
 Maintainers: "Boutros Lab Infrastructure [email protected]"
 Contributors: ["Yael Berkovich", "Tim Sanders"]
 Languages: ["Nextflow", "Docker"]
-Dependencies: ["Java", "Nextflow", "Docker", "Slurm"]
+Dependencies: ["Java", "Nextflow", "Docker"]
 References: "https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Guide+to+Nextflow"
-Tools: ["Delly:v0.8.7", "BCFtools:v1.11", "VCFtools:v0.1.16", "RTG-tools:v3.11", "Validate-nf:v2.1.0"]
+Tools: ["Delly:v0.8.7", "BCFtools:v1.12", "VCFtools:v0.1.16", "RTG-tools:v3.12", "Validate-nf:v2.1.0"]
 Engineering_Owner: []
 Scientific_Owner: []
diff --git a/pipeline/config/methods.config b/pipeline/config/methods.config
@@ -95,9 +95,9 @@ methods.setup()
 params {
     // Pipeline tool versions
     delly_version = '0.8.7'
-    bcftools_version = '1.11'
+    bcftools_version = '1.12'
     vcftools_version = '0.1.16'
-    rtgtools_version = '3.11'
+    rtgtools_version = '3.12'
     validate_version = '2.1.0'
     sha512_version = '0.1'
 }

diff --git a/pipeline/config/nextflow.config b/pipeline/config/nextflow.config
@@ -6,7 +6,7 @@ manifest {
     author = 'Tim Sanders & Yael Berkovich'
     homePage = 'https://github.com/uclahs-cds/pipeline-call-gSV'
     description = 'A pipeline to call structural variants utilizing Delly'
-    version = '2.1.0'
+    version = '2.2.0'
 }
 
 params {

diff --git a/pipeline/modules/bcftools.nf b/pipeline/modules/bcftools.nf
@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 
-def docker_image_bcftools = "blcdsdockerregistry/call-gsv:bcftools-${params.bcftools_version}"
+def docker_image_bcftools = "blcdsdockerregistry/bcftools:${params.bcftools_version}"
 
 log.info """\
 ------------------------------------

diff --git a/pipeline/modules/delly.nf b/pipeline/modules/delly.nf
@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 
-def docker_image_delly = "blcdsdockerregistry/call-gsv:delly-${params.delly_version}"
+def docker_image_delly = "blcdsdockerregistry/delly:${params.delly_version}"
 
 log.info """\
 ------------------------------------
@@ -86,4 +86,4 @@ process delly_call_cnv {
         --mappability   ${params.mappability_map} \
         $input_bam
     """
-}
+}
diff --git a/pipeline/modules/rtgtools.nf b/pipeline/modules/rtgtools.nf
@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 
-def docker_image_rtgtools = "blcdsdockerregistry/call-gsv:rtgtools-${params.rtgtools_version}"
+def docker_image_rtgtools = "blcdsdockerregistry/rtg-tools:${params.rtgtools_version}"
 
 log.info """\
 ------------------------------------
@@ -36,4 +36,4 @@ process rtgtools_vcfstats {
 
     rtg vcfstats $vcf_sv_file > DELLY-${params.delly_version}_${params.dataset_id}_${bam_sample_name}_stats.txt
     """
-}
+}