I activated codon filtering in profile test_novaseq.
Doing so, I realized that codon filtering required QIIME2 environment, that seemed excessive, so I changed to pandas which seems more appropriate. This is modifying https://github.com/nf-core/ampliseq/pull/575.
I wont be able to merge or modify that PR because I'll be three weeks in holiday, so please, if minor changes are needed, fell free to modify the code and merge in case of a positive review.
PR checklist
[x] This comment contains a description of changes (with reason).
[x] 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 pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/ampliseq branch on the nf-core/test-datasets repository.
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[x] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[x] README.md is updated (including new tool citations and authors/contributors).
I activated codon filtering in profile
test_novaseq
. Doing so, I realized that codon filtering required QIIME2 environment, that seemed excessive, so I changed to pandas which seems more appropriate. This is modifying https://github.com/nf-core/ampliseq/pull/575.I wont be able to merge or modify that PR because I'll be three weeks in holiday, so please, if minor changes are needed, fell free to modify the code and merge in case of a positive review.
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).