Merge pull request #68 from luslab/dev

    steps:

      - 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

        with:

          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}

The pipeline has been developed with continuous integration (CI) in mind. nf-core code and module linting as well as a battery of over 100 unit and integration tests run on pull request to the main repository and on release of the pipeline. On official release, automated CI tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/cutandrun/results).

![pipeline_diagram](docs/images/cutandrun-flow-diagram-v1-0_2.png)

## Pipeline summary

1. Check input files

    - picard

    - custom_content

custom_content:

  order:

    - fragment_lengths

    - software_versions

    - software_versions_unique

# Don't show % Dups in the General Stats table (we have this from Picard)

table_columns_visible:

    FastQC:

*/

process {

    // TODO nf-core: Check the defaults for all processes

    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }

    memory = { check_max( 6.GB * task.attempt, 'memory' ) }

    time   = { check_max( 4.h  * task.attempt, 'time'   ) }

    maxRetries    = 1

    maxErrors     = '-1'

    // Process-specific resource requirements

    // NOTE - Please try and re-use the labels below as much as possible.

    //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.

    //        If possible, it would be nice to keep the same label naming convention when

    //        adding in your local modules too.

    // TODO nf-core: Customise requirements for specific processes.

    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors

    withLabel:process_low {

        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }

        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }