Template update for nf-core/tools version 1.13

workflows:

  - subclass: nfl

    primaryDescriptorPath: /nextflow.config

    publish: True

### Default processes resource requirements

Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.

Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.

The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.

## Container engine

- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->

- 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] -->

---

name: Feature request

about: Suggest an idea for the nf-core website

about: Suggest an idea for the nf-core/cutandrun pipeline

labels: enhancement

---

    types: [completed]

  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:

    name: Run AWS full tests

        # 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

        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 }}

        run: |

          aws batch submit-job \

            --region eu-west-1 \