Template update for nf-core/tools version 2.3

name: Bug report

description: Report something that is broken or incorrect

labels: bug

    - [ ] 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`).

- [ ] 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.

    runs-on: ubuntu-latest

    steps:

      - name: Launch workflow via tower

        uses: nf-core/tower-action@v2

        uses: nf-core/tower-action@v3

        # 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

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

            }

          profiles: test_full,aws_tower

          pre_run_script: 'export NXF_VER=21.10.3'

          nextflow_config: |

            process.errorStrategy = 'retry'

            process.maxRetries = 3

    runs-on: ubuntu-latest

    steps:

      - name: Launch workflow via tower

        uses: nf-core/tower-action@v2

        uses: nf-core/tower-action@v3

        with:

          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}

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

            }

          profiles: test,aws_tower

          pre_run_script: 'export NXF_VER=21.10.3'

          nextflow_config: |

            process.errorStrategy = 'retry'

            process.maxRetries = 3

jobs:

  test:

    name: Run workflow tests

    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/cutandrun') }}

    runs-on: ubuntu-latest

        # For example: adding multiple test runs with different parameters

        # Remember that you can parallelise this by using strategy.matrix

        run: |

          nextflow run ${GITHUB_WORKSPACE} -profile test,docker

          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results