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Use alt codes #19

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@hverdonk hverdonk commented Dec 5, 2025 •
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PR checklist

  • 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 necessary, add a test dataset to the test_data directory.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

New Features

  • added support for user-selectable genetic codes --code [CODE], other than the Universal code. A full list of available codes can be found in README.md
  • added new tests and test data
    • tests/test_data/mito_mouse_ref.fasta: reference sequences for the mouse mitochondrial COXI and Cytb genes, ready for workflow input
    • tests/test_data/mito_raw_seqsfasta: vertebrate gene sequences for the mitochondrial COXI and Cytb genes. Pulled from Genbank, ready for workflow input.

hverdonk added 27 commits October 29, 2025 12:47
@hverdonk
first pass at adding support for alternate genetic codes
fd64850
@hverdonk
removed extraneous comments
33aff61
@hverdonk
removed references to nonexistent nf-core/capheine resources
f822528
@hverdonk
updated multiqc module to latest version
4ee6387
@hverdonk
nf-core version update and linting cleanup
0b87b3d
@hverdonk
removed more references to nf-core
319f259
@hverdonk
linting and cleanup
25b8bbd
@hverdonk
removed unused tests, clarified relationship to nf-core in README
56d41bf
@hverdonk
fixes to quiet the test suite
bce231b
@hverdonk
version bump in preparation for initial release
a01d77f
@hverdonk
temporarily test conda and singularity on dev
d4b4c69
@hverdonk
attempt #1 to solve CI test file lock race condition
a22c618
@hverdonk
attempt #2 to solve CI race condition
4c8a3c8
@hverdonk
update minimum required nextflow version, prettier version update
4f26fd4
@hverdonk
added new CODE param tests + a mitochondrial sequence alignment
9113fe1
@hverdonk
updated documentation with the CODE parameter
fc5478b
@hverdonk
module tests for specifying genetic code via translation table number
21ff8e1
@hverdonk
added mito gene test data
0b7d00a
@hverdonk
module test refactoring, drafted additional test
1052314
@hverdonk
updated module to accept hyphy genetic code naming scheme. Module tes…
1c828c4 
…ts passing
@hverdonk
added pipeline-level validation of user-provided genetic code
34dba7e
@hverdonk
tweaking and fixing code choice test
59e19cf
@hverdonk
multiqc version bump
a427130
@hverdonk
version bump and genetic code selection for cawlign
03e59d5
@hverdonk
fixed usage docs
f85f9ea
@hverdonk
pipeline version bump
98cb172
@hverdonk
un-commented test data
59c9226
@hverdonk hverdonk requested a review from d-callan December 5, 2025 20:47
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@hverdonk