Merge pull request #320 from nf-core/dev

Release 2.2.0
nf-core · Mar 13, 2023 · 58afbbc · 58afbbc
2 parents 6ffe304 + 881bec5
commit 58afbbc
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -0,0 +1,27 @@
+{
+    "name": "nfcore",
+    "image": "nfcore/gitpod:latest",
+    "remoteUser": "gitpod",
+
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/opt/conda/bin/python",
+                "python.linting.enabled": true,
+                "python.linting.pylintEnabled": true,
+                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
+                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
+                "python.linting.flake8Path": "/opt/conda/bin/flake8",
+                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
+                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
+                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+            },
+
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
+}
diff --git a/.editorconfig b/.editorconfig
@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js}]
+[*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

diff --git a/.gitattributes b/.gitattributes
@@ -1,3 +1,4 @@
 *.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -101,3 +101,19 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
+
+## GitHub Codespaces
+
+This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+
+To get started:
+
+- Open the repo in [Codespaces](https://github.com/nf-core/rnafusion/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
+- [Dockerfile](.devcontainer/Dockerfile)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -42,7 +42,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 21.10.3)_
+        * Nextflow version _(eg. 22.10.1)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnaf
 
 - [ ] 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/rnafusion/tree/master/.github/CONTRIBUTING.md)
-  - [ ] If necessary, also make a PR on the nf-core/rnafusion _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/rnafusion/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/rnafusion _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.

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -13,7 +13,7 @@ jobs:
     if: github.repository == 'nf-core/rnafusion'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch build workflow via tower
+      - name: Launch build arriba workflow via tower
         uses: nf-core/tower-action@v3
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -22,13 +22,173 @@ jobs:
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "arriba": true,
+              "build_references": true
             }
-          profiles: test_full_build,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3
-      - name: Launch workflow via tower
+          profiles: test_full,aws_tower
+
+      - name: Launch arriba workflow via tower
+        uses: nf-core/tower-action@v3
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "arriba": true,
+            }
+          profiles: test_full,aws_tower
+
+      - name: Launch build squid workflow via tower
+        uses: nf-core/tower-action@v3
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "squid": true,
+              "build_references": true
+            }
+          profiles: test_full,aws_tower
+
+      - name: Launch squid workflow via tower
+        uses: nf-core/tower-action@v3
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "squid": true,
+            }
+          profiles: test_full,aws_tower
+
+      - name: Launch build starfusion workflow via tower
+        uses: nf-core/tower-action@v3
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "starfusion": true,
+              "build_references": true
+            }
+          profiles: test_full,aws_tower
+
+      - name: Launch starfusion workflow via tower
+        uses: nf-core/tower-action@v3
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "starfusion": true,
+            }
+          profiles: test_full,aws_tower
+
+      - name: Launch build fusioncatcher workflow via tower
+        uses: nf-core/tower-action@v3
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "fusioncatcher": true,
+              "build_references": true
+            }
+          profiles: test_full,aws_tower
+
+      - name: Launch fusioncatcher workflow via tower
+        uses: nf-core/tower-action@v3
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "fusioncatcher": true,
+            }
+          profiles: test_full,aws_tower
+
+      - name: Launch build pizzly workflow via tower
+        uses: nf-core/tower-action@v3
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "pizzly": true,
+              "build_references": true
+            }
+          profiles: test_full,aws_tower
+
+      - name: Launch pizzly workflow via tower
+        uses: nf-core/tower-action@v3
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "pizzly": true,
+            }
+          profiles: test_full,aws_tower
+
+      - name: Launch stringtie workflow via tower
         uses: nf-core/tower-action@v3
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -37,6 +197,10 @@ jobs:
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
+              "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
+              "cosmic_username": "${{ secrets.cosmic_username }}",
+              "cosmic_passwd": "${{ secrets.cosmic_passwd }}",
+              "stringtie": true,
             }
           profiles: test_full,aws_tower