New align dedup bwamem

[eduard-watchmaker]

PR checklist

Closes #XXX

• 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 - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[vagkaratzas]

Getting there. Can you please follow this convention for nf-test tags:

    tag "subworkflows"
    tag "subworkflows_nfcore"
    tag "subworkflows/{{ component_name }}"
    // TODO nf-core: Add tags for all modules used within this subworkflow. Example:
    tag "samtools"
    tag "samtools/sort"
    tag "samtools/index"
    tag "subworkflows/{{ component_name_2 }}"
    tag "bwa"
    tag "bwa/index"
    tag "bwa/mem"

Start with your subworkflow and then go in the deeper levels, each time tagging each subworkflow and its components they way they are sourced.

[vagkaratzas]

Good!