Updating contribution docs

Author: Amanda Sullivan

.github/CONTRIBUTING.md

@@ -1,20 +1,20 @@
-# mira/cli: Contributing Guidelines
+# mira-nf/mira: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving mira/cli.
+Many thanks for taking an interest in improving mira-nf/mira.
 
-We try to manage the required tasks for mira/cli using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for mira-nf/mira 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 ;)
 
 ## Contribution workflow
 
-If you'd like to write some code for mira/cli, the standard workflow is as follows:
+If you'd like to write some code for mira-nf/mira, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [mira/cli issues](https://github.com/mira/cli/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 [mira/cli repository](https://github.com/mira/cli) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [mira-nf/mira issues](https://github.com/CDCgov/MIRA-NF/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 [mira-nf/mira repository](https://github.com/CDCgov/MIRA-NF) 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
@@ -58,7 +58,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Pipeline contribution conventions
 
-To make the mira/cli 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 mira-nf/mira 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
 
@@ -108,7 +108,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/mira/cli/codespaces)
+- Open the repo in [Codespaces](https://github.com/mira-nf/mira/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,21 +1,21 @@
 <!--
-# mira/cli pull request
+# mira-nf/mira pull request
 
-Many thanks for contributing to mira/cli!
+Many thanks for contributing to mira-nf/mira!
 
 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.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/mira/cli/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/mira-nf/mira/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/mira/cli/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/CDCgov/MIRA-NF/tree/master/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core 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>`).

.github/workflows/branch.yml

@@ -11,9 +11,9 @@ jobs:
     steps:
       # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'mira/cli'
+        if: github.repository == 'mira-nf/mira'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == mira/cli ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == mira-nf/mira ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $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

.github/workflows/ci.yml

@@ -19,7 +19,7 @@ jobs:
   test:
     name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'mira/cli') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'mira-nf/mira') }}"
     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 == 'mira/cli'
+      github.repository == 'mira-nf/mira'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
@@ -86,4 +86,4 @@ jobs:
           issue-number: ${{ github.event.issue.number }}
           body: |
             @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
-            See [CI log](https://github.com/mira/cli/actions/runs/${{ github.run_id }}) for more details.
+            See [CI log](https://github.com/mira-nf/mira/actions/runs/${{ github.run_id }}) for more details.

CITATIONS.md

@@ -1,4 +1,4 @@
-# mira/cli: Citations
+# mira-nf/mira: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)