From 0ba5d1ec42a35ff55e348456f223fe0d83a48cf2 Mon Sep 17 00:00:00 2001 From: Mohammed Faizal Eeman Mootor <68152431+Faizal-Eeman@users.noreply.github.com> Date: Thu, 14 Jul 2022 18:12:18 -0700 Subject: [PATCH] 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 --- .github/PULL_REQUEST_TEMPLATE.md | 73 +++++++++++++++++--------------- CHANGELOG.md | 4 -- pipeline/nextflow.config | 6 +-- 3 files changed, 42 insertions(+), 41 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index df06f29f..0f5c4af9 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,43 +1,48 @@ - +# Description + -- [ ] 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: + - input csv: + - config: + - output: +- Delly - gSV + - sample: + - input csv: + - config: + - output: +- Delly - gCNV + - sample: + - input csv: + - config: + - output: +- Delly - gSV & gCNV + - sample: + - input csv: + - config: + - output: -- [ ] 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 + -- [ ] 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). - +- [ ] 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: - - input csv: - - config: - - output: -- Delly - gSV - - sample: - - input csv: - - config: - - output: -- Delly - gCNV - - sample: - - input csv: - - config: - - output: -- Delly - gSV & gCNV - - sample: - - input csv: - - config: - - output: +- [ ] 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 index 43b4f66e..740cc5b3 100644 --- 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 index 37bb013b..65d93715 100644 --- 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' -} \ No newline at end of file +}