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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>
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<!--- 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). | ||
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||
- [ ] 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. | ||
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**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. |
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