merge dsl2 into dev

.editorconfig

@@ -0,0 +1,27 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{yml,yaml}]
+indent_size = 2
+
+[*.json]
+insert_final_newline = unset
+
+# These files are edited and tested upstream in nf-core/modules
+[/modules/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+
+[/assets/email*]
+indent_size = unset

.github/CODEOWNERS

@@ -1 +1 @@
-*   @MaxUlysse
+*   @maxulysse

.github/CONTRIBUTING.md

@@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/sarek, the standard workflow is as
     * 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/sarek repository](https://github.com/nf-core/sarek) 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).
+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
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -69,12 +69,12 @@ If you wish to contribute a new step, please use the following coding standards:
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new flags/options to `nextflow.config` with a default (see below).
-5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`).
+5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`).
 6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
 7. Add sanity checks for all relevant parameters.
 8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
 9. Do local tests that the new code works properly and as expected.
-10. Add a new test command in `.github/workflow/ci.yaml`.
+10. Add a new test command in `.github/workflow/ci.yml`.
 11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
 12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
 13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
@@ -83,7 +83,7 @@ If you wish to contribute a new step, please use the following coding standards:
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-Once there, use `nf-core schema build .` to add to `nextflow_schema.json`.
+Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,9 +1,7 @@
 ---
 name: Bug report
 about: Report something that is broken or incorrect
-title: "[BUG]"
 labels: bug
-assignees: maxulysse
 ---
 
 <!--
@@ -53,13 +51,12 @@ Have you provided the following extra information/files:
 
 ## Nextflow Installation
 
-- Version: <!-- [e.g. 19.10.0] -->
+- Version: <!-- [e.g. 21.04.0] -->
 
 ## Container engine
 
 - Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
 - version: <!-- [e.g. 1.0.0] -->
-- Image tag: <!-- [e.g. nfcore/sarek:2.7] -->
 
 ## Additional context
 

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,9 +1,7 @@
 ---
 name: Feature request
 about: Suggest an idea for the nf-core/sarek pipeline
-title: "[FEATURE]"
 labels: enhancement
-assignees: maxulysse
 ---
 
 <!--

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,10 +16,9 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sare
 
 - [ ] 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 - add to the software_versions process and a regex to `scrape_software_versions.py`
     - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
     - [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
-- [ ] Make sure your code lints (`nf-core lint .`).
+- [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

.github/RELEASE_CHECKLIST.md

@@ -3,26 +3,26 @@
 > This checklist is for our own reference, to help us prepare a new release
 
 1. Check that everything is ready to go
-   - Desired [PRs](https://github.com/nf-core/sarek/pulls) are merged
-   - [GitHub Actions](https://github.com/nf-core/sarek/actions?query=workflow%3A%22nf-core+CI%22) are passing on `dev`
-   - [nf-core linting](https://github.com/nf-core/sarek/actions?query=workflow%3A%22nf-core+linting%22) are passing on `dev`
+    - Desired [PRs](https://github.com/nf-core/sarek/pulls) are merged
+    - [GitHub Actions](https://github.com/nf-core/sarek/actions?query=workflow%3A%22nf-core+CI%22) are passing on `dev`
+    - [nf-core linting](https://github.com/nf-core/sarek/actions?query=workflow%3A%22nf-core+linting%22) are passing on `dev`
 2. Increase version number following [semantic versioning](http://semver.org/spec/v2.0.0.html)
 3. Choose an appropriate codename for the release (if major or minor)
-   - i.e. Peaks in [Sarek National Park](https://en.wikipedia.org/wiki/Sarek_National_Park#Topography)
+    - i.e. Peaks in [Sarek National Park](https://en.wikipedia.org/wiki/Sarek_National_Park#Topography)
 4. Sync `dev` and checkout a new branch for the release
 5. Bump version:
-   - `nf-core bump-version . <VERSION>`
-   - edit `.circleci/config.yml`
-   - edit `.github/workflows/ci.yml`
-   - edit `conf/base.config`
-   - edit `conf/test.config`
-   - edit `containers/snpeff/Dockerfile`
-   - edit `containers/snpeff/environment.yml`
-   - edit `containers/vep/Dockerfile`
-   - edit `containers/vep/environment.yml`
-   - edit `docs/images/sarek_workflow.svg`
-   - generate a new `docs/images/sarek_workflow.png`
-   - edit `CHANGELOG`
+    - `nf-core bump-version . <VERSION>`
+    - edit `.circleci/config.yml`
+    - edit `.github/workflows/ci.yml`
+    - edit `conf/base.config`
+    - edit `conf/test.config`
+    - edit `containers/snpeff/Dockerfile`
+    - edit `containers/snpeff/environment.yml`
+    - edit `containers/vep/Dockerfile`
+    - edit `containers/vep/environment.yml`
+    - edit `docs/images/sarek_workflow.svg`
+    - generate a new `docs/images/sarek_workflow.png`
+    - edit `CHANGELOG`
 6. Make a PR to `master`
 7. Wait for reviews
 8. Merge said PR

.github/workflows/awsfulltest.yml

@@ -1,46 +1,34 @@
 name: nf-core AWS full size tests
 # This workflow is triggered on published releases.
-# It can be additionally triggered manually with GitHub actions workflow dispatch.
+# It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  workflow_run:
-    workflows: ["nf-core Docker push (release)"]
-    types: [completed]
+  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 }}
-
-
 jobs:
-  run-awstest:
+  run-tower:
     name: Run AWS full tests
     if: github.repository == 'nf-core/sarek'
     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
+      - name: Launch workflow via tower
+        uses: nf-core/tower-action@master
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
-        # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
-        run: |
-          aws batch submit-job \
-            --region eu-west-1 \
-            --job-name nf-core-sarek \
-            --job-queue $AWS_JOB_QUEUE \
-            --job-definition $AWS_JOB_DEFINITION \
-            --container-overrides '{"command": ["nf-core/sarek", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/sarek/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/sarek/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          pipeline: ${{ github.repository }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}"
+            }
+          profiles: '[ "test_full", "aws_tower" ]'
+

.github/workflows/awstest.yml

@@ -1,42 +1,28 @@
 name: nf-core AWS test
-# This workflow is triggered on push to the master branch.
-# It can be additionally triggered manually with GitHub actions workflow dispatch.
-# It runs the -profile 'test' on AWS batch.
+# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
+# It runs the -profile 'test' on AWS batch
 
 on:
   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 }}
-
-
 jobs:
-  run-awstest:
+  run-tower:
     name: Run AWS tests
     if: github.repository == 'nf-core/sarek'
     runs-on: ubuntu-latest
     steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Launch workflow via tower
+        uses: nf-core/tower-action@master
+
         with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
-        run: |
-          aws batch submit-job \
-          --region eu-west-1 \
-          --job-name nf-core-sarek \
-          --job-queue $AWS_JOB_QUEUE \
-          --job-definition $AWS_JOB_DEFINITION \
-          --container-overrides '{"command": ["nf-core/sarek", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/sarek/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/sarek/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          pipeline: ${{ github.repository }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}"
+            }
+          profiles: '[ "test", "aws_tower" ]'
+