feat: update GitHub templates (#24)

### Changed

- PR template
- PR checklist message body
- Feature request template to include the relevant sections of a User
Story
- Bug report template
- Added the follwoing files to list of files to ignore in linting
config:
	- `.github/ISSUE_TEMPLATE/feature_request.yml`
	- `.github/PULL_REQUEST_TEMPLATE`
	- `.github/ISSUE_TEMPLATE/config.yml`
	- `.github/ISSUE_TEMPLATE/bug_report.yml`
- Updated issue template chooser `.github/ISSUE_TEMPLATE/config.yml` to
include blank issues and remove nf-core contact links

Author: beatrizsavinhas

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -1,40 +1,38 @@
 name: Bug report
-description: Report something that is broken or incorrect
-labels: bug
+labels: ["Bug"]
+projects: ["Clinical-Genomics/108"]
 body:
-  - type: markdown
-    attributes:
-      value: |
-        Before you post this issue, please check the documentation:
-
-        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-        - [nf-core/oncorefiner pipeline documentation](https://nf-co.re/oncorefiner/usage)
   - type: textarea
-    id: description
     attributes:
-      label: Description of the bug
+      label: Description
       description: A clear and concise description of what the bug is.
     validations:
       required: true
 
   - type: textarea
-    id: command_used
     attributes:
-      label: Command used and terminal output
-      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
-      render: console
-      placeholder: |
-        $ nextflow run ...
+      label: How to reproduce
+      description: Steps to reproduce the behaviour. If relevant, please paste the command you used to launch the pipeline and the output from your terminal.
+    validations:
+      required: true
 
-        Some output where something broke
+  - type: textarea
+    attributes:
+      label: Expected behaviour
+      description: A clear and concise description of what you expected to happen.
+    validations:
+      required: false
 
   - type: textarea
-    id: files
     attributes:
-      label: Relevant files
+      label: Anything else?
       description: |
+        Links? Screenshots? Anything that will give us more context about the issue you are encountering!
+
         Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
         Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+    validations:
+      required: false
 
   - type: textarea
     id: system
@@ -46,4 +44,5 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of nf-core/oncorefiner _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of oncorefiner _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of nf-core/oncoanalyser _(eg. 1.1, 1.5, 1.8.2)_

.github/ISSUE_TEMPLATE/config.yml

@@ -1,7 +1 @@
-contact_links:
-  - name: Join nf-core
-    url: https://nf-co.re/join
-    about: Please join the nf-core community here
-  - name: "Slack #oncorefiner channel"
-    url: https://nfcore.slack.com/channels/oncorefiner
-    about: Discussion about the nf-core/oncorefiner pipeline
+blank_issues_enabled: true

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,11 +1,46 @@
 name: Feature request
-description: Suggest an idea for the nf-core/oncorefiner pipeline
-labels: enhancement
+description: User story
+labels: ["User-Story"]
+projects: ["Clinical-Genomics/108"]
 body:
   - type: textarea
-    id: description
     attributes:
-      label: Description of feature
-      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+      label: Need
+      description: Describe the need from the perspective of the user.
+      value: |
+        As a <role>,
+        I want <functionality>
+        because of <reason>.
     validations:
       required: true
+  - type: textarea
+    attributes:
+      label: Acceptance criteria
+      description: |
+        List the requirements needed for this feature to be implemented.
+        If you are unsure, apply label the "Needs Refinement" to the issue.
+      value: |
+        - [ ] <acceptance criterion>
+        - [ ] <acceptance criterion>
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Additional information
+      description: |
+        Please provide any information that can give us more context about this issue.
+      value: |
+        - Suggested approach
+        <!-- Any ideas on how this should be implemented? -->
+
+        - Considered alternatives
+        <!-- Were there alternative approaches which have been rejected? -->
+
+        - Blockers
+        <!-- Anything preventing this from happening?
+
+        - Other notes
+        <!-- Links? References? -->
+    validations:
+      required: false

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,26 +1,15 @@
-<!--
-# nf-core/oncorefiner pull request
+### Added
 
-Many thanks for contributing to nf-core/oncorefiner!
+-
 
-Please fill in the appropriate checklist below (delete whatever is not relevant).
-These are the most common things requested on pull requests (PRs).
+### Changed
 
-Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
+-
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/oncorefiner/tree/master/.github/CONTRIBUTING.md)
--->
+### Fixed
 
-## PR checklist
+-
 
-- [ ] This comment contains a description of changes (with reason).
-- [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/oncorefiner/tree/master/.github/CONTRIBUTING.md)
-- [ ] If necessary, also make a PR on the nf-core/oncorefiner _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
-- [ ] Make sure your code lints (`nf-core pipelines lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
-- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
-- [ ] Usage Documentation in `docs/usage.md` is updated.
-- [ ] Output Documentation in `docs/output.md` is updated.
-- [ ] `CHANGELOG.md` is updated.
-- [ ] `README.md` is updated (including new tool citations and authors/contributors).
+### Removed
+
+-

.github/pr_checklist_comment_body.md

@@ -3,9 +3,6 @@
 - [ ] Fill in description of the PR and link to any relevant issues.
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
 - [ ] If you've added a new tool, follow the pipeline conventions in the [contribution docs](https://github.com/nf-core/oncorefiner/tree/master/.github/CONTRIBUTING.md).
-- [ ] Make sure your code lints (`nf-core pipelines lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
-- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `README.md` is updated (including new tool citations and authors/contributors).

.nf-core.yml

@@ -9,6 +9,10 @@ lint:
     - assets/nf-core-oncorefiner_logo_light.png
     - docs/images/nf-core-oncorefiner_logo_light.png
     - docs/images/nf-core-oncorefiner_logo_dark.png
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/ISSUE_TEMPLATE/feature_request.yml
+    - .github/PULL_REQUEST_TEMPLATE.md
 nf_core_version: 3.5.2
 repository_type: pipeline
 template:

CHANGELOG.md

@@ -17,6 +17,10 @@ Initial release of nf-core/oncorefiner, created with the [nf-core](https://nf-co
 - Added small test profile. The related test dataset have been added as a branch called oncorefiner under [Clinical-Genomics/test-datasets](https://github.com/Clinical-Genomics/test-datasets/tree/oncorefiner) [#8](https://github.com/Clinical-Genomics/oncorefiner/pull/8)
 - Added CI checks for `Conventional PR title`, `Updated changelog` and `Add PR checklist comment` [#18](https://github.com/Clinical-Genomics/oncorefiner/pull/18)
 
+### Changed
+
+- Updated PR template, PR checklist, feature request template, bug report template and issue template chooser [#24](https://github.com/Clinical-Genomics/oncorefiner/pull/24)
+
 ### `Fixed`
 
 - Removed snv_vcf_tbi and sv_vcf_tbi parameter. VCF indexes are now automatically detected [#9](https://github.com/Clinical-Genomics/oncorefiner/pull/9)