Convert YAML files to 4-space indentation

nf-core · May 11, 2021 · b69a7ef · b69a7ef
1 parent 3ac6b94
commit b69a7ef
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Showing 11 changed files with 441 additions and 444 deletions.
diff --git a/.editorconfig b/.editorconfig
@@ -8,9 +8,6 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{yml,yaml}]
-indent_size = 2
-
 # These files are edited upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset

diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml
@@ -1,6 +1,6 @@
 # Dockstore config version, not pipeline version
 version: 1.2
 workflows:
-  - subclass: nfl
-    primaryDescriptorPath: /nextflow.config
-    publish: True
+    -   subclass: nfl
+        primaryDescriptorPath: /nextflow.config
+        publish: True
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,8 +1,8 @@
 blank_issues_enabled: false
 contact_links:
-  - name: Join nf-core
-    url: https://nf-co.re/join
-    about: Please join the nf-core community here
-  - name: "Slack #rnaseq channel"
-    url: https://nfcore.slack.com/channels/rnaseq
-    about: Discussion about the nf-core/rnaseq pipeline
+    -   name: Join nf-core
+        url: https://nf-co.re/join
+        about: Please join the nf-core community here
+    -   name: "Slack #rnaseq channel"
+        url: https://nfcore.slack.com/channels/rnaseq
+        about: Discussion about the nf-core/rnaseq pipeline
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -4,41 +4,41 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
-  workflow_dispatch:
+    release:
+        types: [published]
+    workflow_dispatch:
 
 env:
-  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+    AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+    AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+    TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+    AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+    AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+    AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
 
 jobs:
-  run-awstest:
-    name: Run AWS full tests
-    if: github.repository == 'nf-core/rnaseq'
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        aligner: ['star_salmon', 'star_rsem', 'hisat2']
-    steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
-        # Do a full-scale run with each of the three aligners
-        run: |
-          aws batch submit-job \
-            --region eu-west-1 \
-            --job-name nf-core-rnaseq \
-            --job-queue $AWS_JOB_QUEUE \
-            --job-definition $AWS_JOB_DEFINITION \
-            --container-overrides '{"command": ["nf-core/rnaseq", "-r '"${GITHUB_SHA}"' -profile test_full --aligner '"${{matrix.aligner}}"' --outdir s3://'"${AWS_S3_BUCKET}"'/rnaseq/results-'"${GITHUB_SHA}"'/aligner_'"${{matrix.aligner}}"' -w s3://'"${AWS_S3_BUCKET}"'/rnaseq/work-'"${GITHUB_SHA}"'/'"${{matrix.aligner}}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+    run-awstest:
+        name: Run AWS full tests
+        if: github.repository == 'nf-core/rnaseq'
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                aligner: ['star_salmon', 'star_rsem', 'hisat2']
+        steps:
+            -   name: Setup Miniconda
+                uses: conda-incubator/setup-miniconda@v2
+                with:
+                    auto-update-conda: true
+                    python-version: 3.7
+            -   name: Install awscli
+                run: conda install -c conda-forge awscli
+            -   name: Start AWS batch job
+                # Do a full-scale run with each of the three aligners
+                run: |
+                    aws batch submit-job \
+                        --region eu-west-1 \
+                        --job-name nf-core-rnaseq \
+                        --job-queue $AWS_JOB_QUEUE \
+                        --job-definition $AWS_JOB_DEFINITION \
+                        --container-overrides '{"command": ["nf-core/rnaseq", "-r '"${GITHUB_SHA}"' -profile test_full --aligner '"${{matrix.aligner}}"' --outdir s3://'"${AWS_S3_BUCKET}"'/rnaseq/results-'"${GITHUB_SHA}"'/aligner_'"${{matrix.aligner}}"' -w s3://'"${AWS_S3_BUCKET}"'/rnaseq/work-'"${GITHUB_SHA}"'/'"${{matrix.aligner}}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
 
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -4,34 +4,34 @@ name: nf-core AWS test
 # It runs the -profile 'test' on AWS batch.
 
 on:
-  workflow_dispatch:
+    workflow_dispatch:
 
 env:
-  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+    AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+    AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+    TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+    AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+    AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+    AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
 
 jobs:
-  run-awstest:
-    name: Run AWS tests
-    if: github.repository == 'nf-core/rnaseq'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
-        run: |
-          aws batch submit-job \
-          --region eu-west-1 \
-          --job-name nf-core-rnaseq \
-          --job-queue $AWS_JOB_QUEUE \
-          --job-definition $AWS_JOB_DEFINITION \
-          --container-overrides '{"command": ["nf-core/rnaseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/rnaseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/rnaseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+    run-awstest:
+        name: Run AWS tests
+        if: github.repository == 'nf-core/rnaseq'
+        runs-on: ubuntu-latest
+        steps:
+            -   name: Setup Miniconda
+                uses: conda-incubator/setup-miniconda@v2
+                with:
+                    auto-update-conda: true
+                    python-version: 3.7
+            -   name: Install awscli
+                run: conda install -c conda-forge awscli
+            -   name: Start AWS batch job
+                run: |
+                    aws batch submit-job \
+                    --region eu-west-1 \
+                    --job-name nf-core-rnaseq \
+                    --job-queue $AWS_JOB_QUEUE \
+                    --job-definition $AWS_JOB_DEFINITION \
+                    --container-overrides '{"command": ["nf-core/rnaseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/rnaseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/rnaseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -2,45 +2,45 @@ 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`
 on:
-  pull_request_target:
-    branches: [master]
+    pull_request_target:
+        branches: [master]
 
 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
-      - name: Check PRs
-        if: github.repository == 'nf-core/rnaseq'
-        run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/rnaseq ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
-
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
-        with:
-          message: |
-            ## This PR is against the `master` branch :x:
-
-            * Do not close this PR
-            * Click _Edit_ and change the `base` to `dev`
-            * This CI test will remain failed until you push a new commit
-
-            ---
-
-            Hi @${{ github.event.pull_request.user.login }},
-
-            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.
-
-            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.
-            Note that even after this, the test will continue to show as failing until you push a new commit.
-
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+    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
+            -   name: Check PRs
+                if: github.repository == 'nf-core/rnaseq'
+                run: |
+                    { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/rnaseq ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+
+
+            # If the above check failed, post a comment on the PR explaining the failure
+            # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
+            -   name: Post PR comment
+                if: failure()
+                uses: mshick/add-pr-comment@v1
+                with:
+                    message: |
+                        ## This PR is against the `master` branch :x:
+
+                        * Do not close this PR
+                        * Click _Edit_ and change the `base` to `dev`
+                        * This CI test will remain failed until you push a new commit
+
+                        ---
+
+                        Hi @${{ github.event.pull_request.user.login }},
+
+                        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.
+
+                        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.
+                        Note that even after this, the test will continue to show as failing until you push a new commit.
+
+                        Thanks again for your contribution!
+                    repo-token: ${{ secrets.GITHUB_TOKEN }}
+                    allow-repeats: false