Update versions for five tools

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,3 +1,9 @@
+> This is a template for UCLA-CDS pipeline developers to create a github pull request template. Things should be adjusted for individual pipeline including:
+> 1. additional checklist items sepecific to the pipeline
+> 2. a description of how testing is expected to be done
+> 3. a template list or table for testing results
+> 4. additional notes wrapped in \<!--- ---> (or \<!-- --\> for inline comments) that help PR submitters to fill in.
+> 5. delete this block of instructional text.
 
 # Description
 <!--- Briefly describe the changes included in this pull request and the paths to the test cases below
@@ -7,21 +13,20 @@
 
 ## Testing Results
 
-- Tumor/Normal Paired Sample:
+- Case 1
     - sample:    <!-- e.g. A-mini S2.T-1, A-mini S2.T-n1 -->
-    - input YAML: <!-- path/to/input.csv -->
+    - input csv: <!-- path/to/input.csv -->
     - config:    <!-- path/to/xxx.config -->
     - output:    <!-- path/to/output -->
-- Tumor-only Sample:
+- Case 2
     - sample:    <!-- e.g. A-mini S2.T-1, A-mini S2.T-n1 -->
-    - input YAML: <!-- path/to/input.csv -->
+    - input csv: <!-- path/to/input.csv -->
     - config:    <!-- path/to/xxx.config -->
     - output:    <!-- path/to/output -->
-- Multi-tumor Sample:
-    - sample:    <!-- e.g. A-mini S2.T-1, A-mini S2.T-n1 -->
-    - input YAML: <!-- path/to/input.csv -->
-    - config:    <!-- path/to/xxx.config -->
+- NFTest
     - output:    <!-- path/to/output -->
+    - log:       <!-- path/to/log -->
+    - cases:     <!-- list of test cases run -->
 
 # Checklist
 <!--- Please read each of the following items and confirm by replacing the [ ] with a [X] --->
@@ -34,7 +39,8 @@
 
 - [ ] I have set up or verified the branch protection rule following the [github standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3190380/GitHub+Standards#GitHubStandards-Branchprotectionrule) before opening this pull request.
 
-- [ ] I have added my name to the contributors listings in the ``manifest`` block in the `nextflow.config` as part of this pull request; I am listed already, or do not wish to be listed. (*This acknowledgement is optional.*)
+- [ ] I have added my name to the contributors listings in the ``manifest`` block in the `nextflow.config` as part of this pull request, am listed
+already, or do not wish to be listed. (*This acknowledgement is optional.*)
 
 - [ ] I have added the changes included in this pull request to the `CHANGELOG.md` under the next release version or unreleased, and updated the date.
 

CHANGELOG.md

@@ -5,6 +5,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+### Changed
+- Update pipeval 4.0.0-rc.2 -> 5.1.0
+- Update GATK 4.5.0.0 -> 4.6.1.0
+- Update bam_readcount 0.8.0 -> 1.0.1
+- Update MuSE 2.0.4 -> MuSE 2.1.2
+- Update BCFtools 1.17 -> 1.21
+- Update NFtest for new tool versions
+
 ### Added
 - Use `methods.setup_process_afterscript()` for process logs
 - Output pipeline parameters to log directory using `store_object_as_json`

config/default.config

@@ -18,23 +18,23 @@ params {
     docker_container_registry = "ghcr.io/uclahs-cds"
 
     //algorithm version
-    pipeval_version = "4.0.0-rc.2"
-    GATK_version = "4.5.0.0"
+    pipeval_version = "5.1.0"
+    GATK_version = "4.6.1.0"
     somaticsniper_version = "1.0.5.0"
-    bam_readcount_version = "0.8.0"
+    bam_readcount_version = "1.0.1"
     ubuntu_version = "20.04"
     strelka2_version = "2.9.10"
     manta_version = "1.6.0"
-    MuSE_version = "2.0.4"
-    BCFtools_version = "1.17"
+    MuSE_version = "2.1.2"
+    BCFtools_version = "1.21"
     call_ssnv_r_version = "dev"
     vcf2maf_version = "v1.6.18"
     bpg_version = "7.1.0"
     src_util_version = "1.2.0"
     docker_image_validate_params = "${-> params.docker_container_registry}/pipeval:${params.pipeval_version}"
     docker_image_GATK = "broadinstitute/gatk:${params.GATK_version}"
     docker_image_somaticsniper = "${-> params.docker_container_registry}/somaticsniper:${params.somaticsniper_version}"
-    docker_image_bam_readcount = "${-> params.docker_container_registry}/bam-readcount:${params.bam_readcount_version}"
+    docker_image_bam_readcount = "${-> params.docker_container_registry}/bam_readcount:${params.bam_readcount_version}"
     docker_image_ubuntu = "ubuntu:${params.ubuntu_version}"
     docker_image_strelka2 = "${-> params.docker_container_registry}/strelka2:${params.strelka2_version}"
     docker_image_manta = "${-> params.docker_container_registry}/manta:${params.manta_version}"

metadata.yaml

@@ -5,4 +5,4 @@ Maintainers: [[email protected]]
 Contributors: ['Mao Tian', 'Bugh Caden', 'Helena Winata', 'Yash Patel', 'Sorel Fitz-Gibbon']
 Languages: ['Docker', 'Nextflow']
 Dependencies: ['Docker', 'Nextflow']
-Tools: ['GATK 4.5.0.0', 'SomaticSniper v1.0.5.0', 'Strelka2 v2.9.10', 'Manta v1.6.0', 'MuSE v2.0.4', 'BCFtools v1.17', 'R v4.3.1', 'VennDiagram v1.7.3', 'vcf2maf v1.6.18']
+Tools: ['GATK 4.6.1.0', 'SomaticSniper v1.0.5.0', 'Strelka2 v2.9.10', 'Manta v1.6.0', 'MuSE v2.1.2', 'BCFtools v1.21', 'R v4.3.1', 'VennDiagram v1.7.3', 'vcf2maf v1.6.18']