add .github files

.github/CONTRIBUTING.md

@@ -1,24 +1,24 @@
-# nf-core/stuffy: Contributing Guidelines
+# mskcc/forte: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving nf-core/stuffy.
+Many thanks for taking an interest in improving mskcc/forte.
 
-We try to manage the required tasks for nf-core/stuffy using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for mskcc/forte using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
 :::info
-If you need help using or modifying nf-core/stuffy then the best place to ask is on the nf-core Slack [#stuffy](https://nfcore.slack.com/channels/stuffy) channel ([join our Slack here](https://nf-co.re/join/slack)).
+If you need help using or modifying mskcc/forte then the best place to ask is on the [FORTE issues page](https://github.com/mskcc/forte/issues).
 :::
 
 ## Contribution workflow
 
-If you'd like to write some code for nf-core/stuffy, the standard workflow is as follows:
+If you'd like to write some code for mskcc/forte, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/stuffy issues](https://github.com/nf-core/stuffy/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/stuffy repository](https://github.com/nf-core/stuffy) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [mskcc/forte issues](https://github.com/mskcc/forte/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [mskcc/forte repository](https://github.com/mskcc/forte) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
@@ -56,11 +56,11 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Getting help
 
-For further information/help, please consult the [nf-core/stuffy documentation](https://nf-co.re/stuffy/usage) and don't hesitate to get in touch on the nf-core Slack [#stuffy](https://nfcore.slack.com/channels/stuffy) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [mskcc/forte documentation](https://github.com/mskcc/forte/blob/main/docs/).
 
 ## Pipeline contribution conventions
 
-To make the nf-core/stuffy code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the mskcc/forte code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
@@ -110,7 +110,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/nf-core/stuffy/codespaces)
+- Open the repo in [Codespaces](https://github.com/mskcc/forte/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -8,7 +8,7 @@ body:
         Before you post this issue, please check the documentation:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-        - [nf-core/stuffy pipeline documentation](https://nf-co.re/stuffy/usage)
+        - [mskcc/forte pipeline documentation](https://github.com/mskcc/forte/tree/main/docs)
 
   - type: textarea
     id: description
@@ -47,4 +47,4 @@ 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/stuffy _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of mskcc/forte _(eg. 1.1, 1.5, 1.8.2)_

.github/ISSUE_TEMPLATE/config.yml

@@ -2,6 +2,3 @@ contact_links:
   - name: Join nf-core
     url: https://nf-co.re/join
     about: Please join the nf-core community here
-  - name: "Slack #stuffy channel"
-    url: https://nfcore.slack.com/channels/stuffy
-    about: Discussion about the nf-core/stuffy pipeline

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the nf-core/stuffy pipeline
+description: Suggest an idea for the mskcc/forte pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,22 +1,22 @@
 <!--
-# nf-core/stuffy pull request
+# mskcc/forte pull request
 
-Many thanks for contributing to nf-core/stuffy!
+Many thanks for contributing to mskcc/forte!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
-Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
+Remember that PRs should be made against the develop branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/stuffy/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/mskcc/forte/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## 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/stuffy/tree/master/.github/CONTRIBUTING.md)
-- [ ] If necessary, also make a PR on the nf-core/stuffy _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/mskcc/forte/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the mskcc/forte _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/awsfulltest.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   run-tower:
     name: Run AWS full tests
-    if: github.repository == 'nf-core/stuffy'
+    if: github.repository == 'mskcc/forte'
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
@@ -23,11 +23,11 @@ jobs:
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/stuffy/work-${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/forte/work-${{ github.sha }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/stuffy/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/forte/results-${{ github.sha }}"
             }
           profiles: test_full
 

.github/workflows/awstest.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   run-tower:
     name: Run AWS tests
-    if: github.repository == 'nf-core/stuffy'
+    if: github.repository == 'mskcc/forte'
     runs-on: ubuntu-latest
     steps:
       # Launch workflow using Tower CLI tool action
@@ -18,10 +18,10 @@ jobs:
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/stuffy/work-${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/forte/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/stuffy/results-test-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/forte/results-test-${{ github.sha }}"
             }
           profiles: test
 

.github/workflows/branch.yml

@@ -1,6 +1,6 @@
 name: nf-core branch protection
 # This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# It fails when someone tries to make a PR against the nf-core `master` branch instead of `develop`
 on:
   pull_request_target:
     branches: [master]
@@ -9,11 +9,11 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `develop` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'nf-core/stuffy'
+        if: github.repository == 'mskcc/forte'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/stuffy ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == mskcc/forte ]] && [[ $GITHUB_HEAD_REF == "develop" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
@@ -25,7 +25,7 @@ jobs:
             ## This PR is against the `master` branch :x:
 
             * Do not close this PR
-            * Click _Edit_ and change the `base` to `dev`
+            * Click _Edit_ and change the `base` to `develop`
             * This CI test will remain failed until you push a new commit
 
             ---
@@ -34,9 +34,9 @@ jobs:
 
             It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
             The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `develop` branch.
 
-            You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
+            You do not need to close this PR, you can change the target branch to `develop` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.
 
             Thanks again for your contribution!

.github/workflows/ci.yml

@@ -3,7 +3,7 @@ name: nf-core CI
 on:
   push:
     branches:
-      - dev
+      - develop
   pull_request:
   release:
     types: [published]
@@ -18,8 +18,8 @@ concurrency:
 jobs:
   test:
     name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/stuffy') }}"
+    # Only run on push if this is the nf-core develop branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'mskcc/forte') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:

.github/workflows/fix-linting.yml

@@ -9,7 +9,7 @@ jobs:
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
-      github.repository == 'nf-core/stuffy'
+      github.repository == 'mskcc/forte'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later

.github/workflows/linting.yml

@@ -5,7 +5,7 @@ name: nf-core linting
 on:
   push:
     branches:
-      - dev
+      - develop
   pull_request:
   release:
     types: [published]