Development documentation

Adding new profile workflow

• Installed modules nf-core modules install <tool>/<subtool>
• Added parameters to nextflow.config
  • Added --build_<profiler>
  • Added --<profiler>_build_params
  • Added other profiler-specific parameters (e.g. additional taxonomy files)
  • Format with VSCode Nextflow extension
• Added tools(s) to workflow/createtaxdb.nf
  • Added relevant new input files to take: block, and pass into from main.nf to the NFCORE_CREATETAXDB workflow
  • Added relevant modules/subworkflows at the top using include statement
  • Add the tool into the PREPROCESSING subworkflow’s PREPARE if/else (contatenation) section
  • Added the tool-specific if/else statement in the main createtaxdb.nf
  • Version and MultiQC (if available) channels mixed
  • Include output channel in workflow emit statement
  • Format with VSCode Nextflow extension
• Update modules.conf if additional customisation required
  • Added withName: block
  • Added ext.args = ${params.<profiler>_build_params}
  • Added other args (ext.args) based on additional profiler specific parameters modules
  • Format with VSCode Nextflow extension
• If necessary, added any profiler-specific parameter validation checks to utils_nfcore_createtaxdb_pipeline and possible at the top of createtaxdb.nf
• Update tests
  • Include the tool in the test_minimal.config (as false), test.config, test_nothing.config, and test_full.config
  • Do a mini test of test_minimal to make sure it executes when sole tool
  • Format these files with VSCode Nextflow extension
  • Include the output object in the tests/test.nf.test file
  • Re-run nf-test to update snapshot: nf-test test --tag test --profile +docker --updateSnapshot (tip: for assertions, borrow from the modules assertions!)
• Updated Documentation
  • nf-core pipelines schema build has been run and updated
    • All additional tool specific pipeline parameters have a additional help entry with the Modifies tool parameter(s) quote block
  • Added citation to citations.md (citation style: APA 7th edition)
  • Add citation to the toolCitation/BibliographyText functions in utils_nfcore_createtaxdb_pipeline subworkflow
    • Added in-text citation
    • Added bibliography (citation style: APA 7th edition)
  • Added relevant documentation to usage.md
    • Add line to FAQ of recommended auxiliary files (if required)
  • Described module output in output.md
    • Entry in table of contents
    • Entry describing output file and how to supply it to the downstream classification tool
  • Added to pipeline summary list on README.md
  • Added to pipeline metro map diagram
  • If it’s your first contribution, add or move yourself to the Team list on README.md!
• Test(s) pass