updated traceback subworkflow and associated modules with changes for…

[rnaidu]

… nucleovar version 1

PR checklist

• Updating traceback subworkflow and associated modules with changes reflected in nucleovar version 1
• Check to see if a nf-core module, or subworkflow is available and usable for your pipeline.
• Feature branch is named feature/<module_name> for modules, or feature/<subworkflow_name> for subworkflows. For modules, if there is a subcommand use: feature/<module_name>/<module_subcommand>.
• 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.
• Use nf-core data if possible for nf-tests. If not, use or add test data to mskcc-omics-workflows/test-datasets, following the repository guidelines, for nf-tests. Finally, if neither option is feasible, only add a stub nf-test.
• 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 Jfrog 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 --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile docker
    • nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile singularity
    • nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile singularity

[rnaidu]

@buehlere updates to traceback subworkflow + modules (so nucleovar v1 can be merged into dev) is ready for review. only check(s) failing are verify-markdown-file checks, which is because of updates to nf-core schema for listing environment and meta.yml files. Leaving verify-markdown-file checks as is until we come to a consensus on which schema the group will use.

refer to #148 (comment) which encountered the same issue