name change for .github workflow files

.github/workflows/awsfulltest.yml

@@ -1,4 +1,4 @@
-name: nf-core AWS full size tests
+name: PolkaPox AWS full size tests
 # This workflow is triggered on published releases.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
@@ -10,7 +10,7 @@ on:
 jobs:
   run-tower:
     name: Run AWS full tests
-    if: github.repository == 'nf-core/mpxvassembly'
+    if: github.repository == 'CDCgov/polkapox'
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower

.github/workflows/awstest.yml

@@ -1,4 +1,4 @@
-name: nf-core AWS test
+name: PolkaPox AWS test
 # This workflow can be triggered manually with the GitHub actions workflow dispatch button.
 # It runs the -profile 'test' on AWS batch
 
@@ -7,7 +7,7 @@ on:
 jobs:
   run-tower:
     name: Run AWS tests
-    if: github.repository == 'nf-core/mpxvassembly'
+    if: github.repository == 'CDCgov/polkapox'
     runs-on: ubuntu-latest
     steps:
       # Launch workflow using Tower CLI tool action

.github/workflows/branch.yml

@@ -1,4 +1,4 @@
-name: nf-core branch protection
+name: PolkaPox 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`
 on:
@@ -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 == 'nf-core/mpxvassembly'
+        if: github.repository == 'CDCgov/polkapox'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/mpxvassembly ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == CDCgov/polkapox ]] && [[ $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

@@ -1,4 +1,4 @@
-name: nf-core CI
+name: PolkaPox CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
   push:
@@ -16,7 +16,7 @@ jobs:
   test:
     name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mpxvassembly') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'CDCgov/polkapox') }}"
     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/mpxvassembly'
+      github.repository == 'CDCgov/polkapox'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later

.github/workflows/linting_comment.yml

@@ -1,10 +1,10 @@
-name: nf-core linting comment
+name: PolkaPox linting comment
 # This workflow is triggered after the linting action is complete
 # It posts an automated comment to the PR, even if the PR is coming from a fork
 
 on:
   workflow_run:
-    workflows: ["nf-core linting"]
+    workflows: ["PolkaPox linting"]
 
 jobs:
   test: