Update PR Template based on NF pipeline template (#50)

* closes #48 - Update PR Template based on NF pipeline template * Update CHANGELOG.md and nextflow.config * replaced double quotes with back-ticks in PULL_REQUEST_TEMPLATE.md * Update CHANGELOG.md * Update pipeline/nextflow.config Co-authored-by: Mootor <mmootor@ip-0A12522C.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>
uclahs-cds · Jul 15, 2022 · 0ba5d1e · 0ba5d1e
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,43 +1,48 @@
-<!--- Please read each of the following items and confirm by replacing
- !--the [ ] with a [X] --->
+# Description
+<!--- Briefly describe the changes included in this pull request and the paths to the test cases below
+ !--- starting with 'Closes #...' if appropriate --->
 
-- [ ] I have read the [code review guidelines](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Guidelines) and the [code review best practice on GitHub check-list](https://confluence.mednet.ucla.edu/pages/viewpage.action?pageId=84091668).
+### Closes #...
 
-- [ ] I have set up the branch protection rule following the [github standards](https://confluence.mednet.ucla.edu/pages/viewpage.action?spaceKey=BOUTROSLAB&title=GitHub+Standards#GitHubStandards-Branchprotectionrule) before opening this pull request, or the branch protection rule has already been set up.
+## Testing Results
 
-- [ ] I have added my name to the contributors listings in the
-``metadata.yaml`` and the ``manifest`` block in the config as part of this pull request, am listed
-already, or do not wish to be listed. (*This acknowledgement is optional.*)
+- Manta
+    - sample:    <!-- e.g. A-mini TWGSAMIN000001-T001-S01-F, TWGSAMIN000001-T002-S02-F -->
+    - input csv: <!-- path/to/input/call-gSV-inputs.csv -->
+    - config:    <!-- path/to/cpnfig/nextflow-test-amini.config -->
+    - output:    <!-- path/to/output/Manta-1.6.0/ -->
+- Delly - gSV
+    - sample:    <!-- e.g. A-mini TWGSAMIN000001-T001-S01-F, TWGSAMIN000001-T002-S02-F -->
+    - input csv: <!-- path/to/input/call-gSV-inputs.csv -->
+    - config:    <!-- path/to/config/nextflow-test-amini.config -->
+    - output:    <!-- path/to/output/Delly-0.8.7/ -->
+- Delly - gCNV
+    - sample:    <!-- e.g. A-mini TWGSAMIN000001-T001-S01-F, TWGSAMIN000001-T002-S02-F -->
+    - input csv: <!-- path/to/input/call-gSV-inputs.csv -->
+    - config:    <!-- path/to/config/nextflow-test-amini.config -->
+    - output:    <!-- path/to/output/Delly-0.8.7/ -->
+- Delly - gSV & gCNV
+    - sample:    <!-- e.g. A-mini TWGSAMIN000001-T001-S01-F, TWGSAMIN000001-T002-S02-F -->
+    - input csv: <!-- path/to/input/call-gSV-inputs.csv -->
+    - config:    <!-- path/to/config/nextflow-test-amini.config -->
+    - output:    <!-- path/to/output/Delly-0.8.7/ -->
 
-- [ ] 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.
+# Checklist
+<!--- Please read each of the following items and confirm by replacing the [ ] with a [X] --->
 
-- [ ] I have updated the version number in the `metadata.yaml` and config file following [semver](https://semver.org/), or the version number has already been updated. (*Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.*)
+- [ ] I have read the [code review guidelines](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Guidelines) and the [code review best practice on GitHub check-list](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Best+Practice+on+GitHub+-+Check+List).
 
-- [ ] I have tested the pipeline on at least one A-mini sample with "run_delly = true", "run_manta = true", "run_qc = true". For run_delly = true, I have tested "variant_type" set to `gSV`, `gCNV`, and both. The paths to the test config files and output directories were attached below.
+- [ ] I have reviewed the [Nextflow pipeline standards](https://confluence.mednet.ucla.edu/pages/viewpage.action?spaceKey=BOUTROSLAB&title=Nextflow+pipeline+standardization).
 
-<!--- Briefly describe the changes included in this pull request and the paths to the test cases below
- !--- starting with 'Closes #...' if appropriate --->
+- [ ] The name of the branch is meaningful and well formatted following the [standards](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Best+Practice+on+GitHub+-+Check+List), using \[AD_username (or 5 letters of AD if AD is too long)]-\[brief_description_of_branch].
 
-Closes #...
+- [ ] I have set up or verified the branch protection rule following the [github standards](https://confluence.mednet.ucla.edu/pages/viewpage.action?spaceKey=BOUTROSLAB&title=GitHub+Standards#GitHubStandards-Branchprotectionrule) before opening this pull request.
 
-**Test Results**
-- Manta
-	- sample:    <!-- e.g. A-mini TWGSAMIN000001-T001-S01-F, TWGSAMIN000001-T002-S02-F -->
-	- input csv: <!-- /hot/pipelines/development/slurm/pipeline-call-gSV/input/call-gSV-inputs.csv -->
-	- config:    <!-- /hot/pipelines/development/slurm/pipeline-call-gSV/config/nextflow-test-amini.config -->
-	- output:    <!-- /hot/pipelines/development/slurm/pipeline-call-gSV/output/Manta-1.6.0 -->
-- Delly - gSV
-	- sample:    <!-- e.g. A-mini TWGSAMIN000001-T001-S01-F, TWGSAMIN000001-T002-S02-F -->
-	- input csv: <!-- /hot/pipelines/development/slurm/pipeline-call-gSV/input/call-gSV-inputs.csv -->
-	- config:    <!-- /hot/pipelines/development/slurm/pipeline-call-gSV/config/nextflow-test-amini.config -->
-	- output:    <!-- /hot/pipelines/development/slurm/pipeline-call-gSV/output/Delly-0.8.7 -->
-- Delly - gCNV
-	- sample:    <!-- e.g. A-mini TWGSAMIN000001-T001-S01-F, TWGSAMIN000001-T002-S02-F -->
-	- input csv: <!-- /hot/pipelines/development/slurm/pipeline-call-gSV/input/call-gSV-inputs.csv -->
-	- config:    <!-- /hot/pipelines/development/slurm/pipeline-call-gSV/config/nextflow-test-amini.config -->
-	- output:    <!-- /hot/pipelines/development/slurm/pipeline-call-gSV/output/Delly-0.8.7 --> 
-- Delly - gSV & gCNV
-	- sample:    <!-- e.g. A-mini TWGSAMIN000001-T001-S01-F, TWGSAMIN000001-T002-S02-F -->
-	- input csv: <!-- /hot/pipelines/development/slurm/pipeline-call-gSV/input/call-gSV-inputs.csv -->
-	- config:    <!-- /hot/pipelines/development/slurm/pipeline-call-gSV/config/nextflow-test-amini.config -->
-	- output:    <!-- /hot/pipelines/development/slurm/pipeline-call-gSV/output/Delly-0.8.7 -->
+- [ ] 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.
+
+- [ ] I have updated the version number in the `metadata.yaml` and `manifest` block of the `nextflow.config` file following [semver](https://semver.org/), or the version number has already been updated. (*Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.*)
+
+- [ ] I have tested the pipeline on at least one A-mini sample with `run_delly = true`, `run_manta = true`, `run_qc = true`. For `run_delly = true`, I have tested 'variant_type' set to `gSV`, `gCNV`, and both. The paths to the test config files and output directories are captured above in the Testing Results section.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,10 +4,6 @@ All notable changes to the call-gSV pipeline.
 ---
 
 ## [Unreleased]
-
----
-
-## [4.0.0-rc.1] - 2022-04-01
 ### Added
 - Add the Issue Report template
 - Add the Pull Request template

diff --git a/pipeline/nextflow.config b/pipeline/nextflow.config
@@ -4,8 +4,8 @@ manifest {
     name = 'call-gSV'
     mainScript = 'call-gSV.nf'
     nextflowVersion = '>=20.07.1'
-    author = 'Yu Pan, Tim Sanders, Yael Berkovich'
+    author = 'Yu Pan, Tim Sanders, Yael Berkovich, Mohammed Faizal Eeman Mootor'
     homePage = 'https://github.com/uclahs-cds/pipeline-call-gSV'
-    description = 'A pipeline to call structural variants utilizing Delly and Manta'
+    description = 'A pipeline to call germline structural variants utilizing Delly and Manta'
     version = '4.0.0-rc.1'
-}
+}