Allow num_chains to be set in the config

[nikhil]

PR checklist

Closes #XXX

• [ ] This comment contains a description of changes (with reason).
• [ ] 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
  • [ ] nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile conda

[nikhil]

NF-core lint requires the schema to be updated but verify markdown uses the older schema, so this needs to wait until we decide on a schema