Merge pull request #43 from jianhong/dev

Dev

.editorconfig

@@ -8,12 +8,9 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{yml,yaml}]
+[*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
-[*.json]
-insert_final_newline = unset
-
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset

.github/CONTRIBUTING.md

@@ -15,8 +15,7 @@ Contributions to the code are even more welcome ;)
 
 If you'd like to write some code for nf-core/hicar, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/hicar issues](https://github.com/nf-core/hicar/issues) to avoid duplicating work
-    * If there isn't one already, please create one so that others know you're working on this
+1. Check that there isn't already an issue about your idea in the [nf-core/hicar issues](https://github.com/nf-core/hicar/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/hicar repository](https://github.com/nf-core/hicar) 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).
@@ -49,9 +48,9 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
-* On your own fork, make a new branch `patch` based on `upstream/master`.
-* Fix the bug, and bump version (X.Y.Z+1).
-* A PR should be made on `master` from patch to directly this particular bug.
+- On your own fork, make a new branch `patch` based on `upstream/master`.
+- Fix the bug, and bump version (X.Y.Z+1).
+- A PR should be made on `master` from patch to directly this particular bug.
 
 ## Getting help
 
@@ -73,7 +72,7 @@ If you wish to contribute a new step, please use the following coding standards:
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
-9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
+9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values
@@ -92,8 +91,8 @@ The process resources can be passed on to the tool dynamically within the proces
 
 Please use the following naming schemes, to make it easy to understand what is going where.
 
-* initial process channel: `ch_output_from_<process>`
-* intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
+- initial process channel: `ch_output_from_<process>`
+- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
 
 ### Nextflow version bumping
 

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,7 +2,6 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-
   - type: markdown
     attributes:
       value: |

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,10 +16,10 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/hica
 
 - [ ] 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/hicar/tree/master/.github/CONTRIBUTING.md)
-    - [ ] If necessary, also make a PR on the nf-core/hicar _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/nf-core/hicar/tree/master/.github/CONTRIBUTING.md)
+  - [ ] If necessary, also make a PR on the nf-core/hicar _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>`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/awstest.yml

@@ -10,9 +10,9 @@ jobs:
     if: github.repository == 'nf-core/hicar'
     runs-on: ubuntu-latest
     steps:
+      # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v3
-
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/branch.yml

@@ -13,8 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/hicar'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/hicar ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
-
+          "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/hicar ]] && [[ $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

@@ -16,19 +16,19 @@ jobs:
   test:
     name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/hicar') }}
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/hicar') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         # Nextflow versions
-        profile: ['test', 'test_full', 'test_hipeak', 'test_hichip']
+        profile: ["test", "test_full", "test_hipeak", "test_hichip"]
         include:
           # Test pipeline minimum Nextflow version
-          - NXF_VER: '21.10.3'
-            NXF_EDGE: ''
+          - NXF_VER: "21.10.3"
+            NXF_EDGE: ""
           # Test latest edge release of Nextflow
-          - NXF_VER: ''
-            NXF_EDGE: '1'
+          - NXF_VER: ""
+            NXF_EDGE: "1"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -46,3 +46,5 @@ jobs:
       - name: Run pipeline with test data
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results
+
+#

.github/workflows/linting.yml

@@ -1,49 +1,14 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
+# It runs the `nf-core lint` and markdown lint tests to ensure
+# that the code meets the nf-core guidelines.
 on:
   push:
   pull_request:
   release:
     types: [published]
 
 jobs:
-  Markdown:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
-      - name: Install markdownlint
-        run: npm install -g markdownlint-cli
-      - name: Run Markdownlint
-        run: markdownlint .
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
-        with:
-          message: |
-            ## Markdown linting is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install `markdownlint-cli`
-                * On Mac: `brew install markdownlint-cli`
-                * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
-            * Fix the markdown errors
-                * Automatically: `markdownlint . --fix`
-                * Manually resolve anything left from `markdownlint .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
-
-            We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
-
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
@@ -55,49 +20,24 @@ jobs:
         run: npm install -g editorconfig-checker
 
       - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
+        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
 
-  YAML:
+  Prettier:
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
-        uses: actions/checkout@master
-      - name: 'Yamllint'
-        uses: karancode/yamllint-github-action@master
-        with:
-          yamllint_file_or_dir: '.'
-          yamllint_config_filepath: '.yamllint.yml'
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
-        with:
-          message: |
-            ## YAML linting is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install `yamllint`
-                * Install `yamllint` following [this](https://yamllint.readthedocs.io/en/stable/quickstart.html#installing-yamllint)
-                instructions or alternative install it in your [conda environment](https://anaconda.org/conda-forge/yamllint)
-            * Fix the markdown errors
-                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml`
-                * Fix any reported errors in your YAML files
+      - uses: actions/checkout@v2
 
-            Once you push these changes the test should pass, and you can hide this comment :+1:
+      - uses: actions/setup-node@v2
 
-            We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+      - name: Install Prettier
+        run: npm install -g prettier
 
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+      - name: Run Prettier --check
+        run: prettier --check ${GITHUB_WORKSPACE}
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
-
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
@@ -110,8 +50,8 @@ jobs:
 
       - uses: actions/setup-python@v1
         with:
-          python-version: '3.6'
-          architecture: 'x64'
+          python-version: "3.6"
+          architecture: "x64"
 
       - name: Install dependencies
         run: |
@@ -138,3 +78,5 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
+
+#

.github/workflows/local_modules.yml

@@ -13,7 +13,7 @@ jobs:
       - uses: dorny/paths-filter@v2
         id: filter
         with:
-          filters: 'tests/config/pytest_software.yml'
+          filters: "tests/config/pytest_software.yml"
 
   test:
     runs-on: ubuntu-latest
@@ -23,9 +23,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        nxf_version: ['21.04.0']
-        tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
-        profile: ['docker', 'singularity'] ## 'conda'
+        nxf_version: ["21.04.0"]
+        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
+        profile: ["docker", "singularity"] ## 'conda'
     env:
       NXF_ANSI_LOG: false
     steps:
@@ -34,7 +34,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: '3.x'
+          python-version: "3.x"
 
       - uses: actions/cache@v2
         with:
@@ -46,7 +46,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: '3.x'
+          python-version: "3.x"
 
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pytest-workflow
@@ -98,3 +98,5 @@ jobs:
             /home/runner/pytest_workflow_*/*/.nextflow.log
             /home/runner/pytest_workflow_*/*/log.out
             /home/runner/pytest_workflow_*/*/log.err
+
+#

.gitpod.yml

@@ -2,13 +2,13 @@ image: nfcore/gitpod:latest
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    - codezombiech.gitignore                 # Language support for .gitignore files
+    - codezombiech.gitignore # Language support for .gitignore files
     # - cssho.vscode-svgviewer                 # SVG viewer
-    - davidanson.vscode-markdownlint         # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - eamodio.gitlens                        # Quickly glimpse into whom, why, and when a line or code block was changed
-    - EditorConfig.EditorConfig              # override user/workspace settings with settings found in .editorconfig files
-    - Gruntfuggly.todo-tree                  # Display TODO and FIXME in a tree view in the activity bar
-    - mechatroner.rainbow-csv                # Highlight columns in csv files in different colors
+    - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
+    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
+    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
     # - nextflow.nextflow                      # Nextflow syntax highlighting
-    - oderwat.indent-rainbow                 # Highlight indentation level
-    - streetsidesoftware.code-spell-checker  # Spelling checker for source code
+    - oderwat.indent-rainbow # Highlight indentation level
+    - streetsidesoftware.code-spell-checker # Spelling checker for source code

.prettierrc.yml

@@ -0,0 +1 @@
+printWidth: 120

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.0dev - [01/25/2022]
 
+- add filters to chromosome names for `hipeak`.
 - add parameter `anchor_peaks`.
 - Update `MAPS` for new version of `VGAM`.
 - add parameter `publish_dir_mode`.