Template update for nf-core/tools version 2.0

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

# 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

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`.

I have checked the following places for your error:

- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)

- [ ] [nf-core/cutandrun pipeline documentation](https://nf-co.re/nf-core/cutandrun/usage)

- [ ] [nf-core/cutandrun pipeline documentation](https://nf-co.re/cutandrun/usage)

## Description of the bug

## 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/cutandrun:1.0.0] -->

## Additional context

- [ ] 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/cutandrun/tree/master/.github/CONTRIBUTING.md)

    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/cutandrun/tree/master/.github/CONTRIBUTING.md)

    - [ ] If necessary, also make a PR on the nf-core/cutandrun _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`).

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/cutandrun'

    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-cutandrun \

            --job-queue $AWS_JOB_QUEUE \

            --job-definition $AWS_JOB_DEFINITION \

            --container-overrides '{"command": ["nf-core/cutandrun", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/cutandrun/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/cutandrun/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://${{ secrets.AWS_S3_BUCKET }}/work/cutandrun/work-${{ github.sha }}

          parameters: |

            {

              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-${{ github.sha }}"

            }

          profiles: '[ "test_full", "aws_tower" ]'