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Make addSpecies optional also when using cut_its #372

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merged 5 commits into from Jan 26, 2022
Merged

Make addSpecies optional also when using cut_its #372

merged 5 commits into from Jan 26, 2022

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jtangrot
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PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • CHANGELOG.md is updated.

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This adresses issue #370
Option --skip_dada_addspecies was not compatible with --cut_its, but now this should be fixed.

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github-actions bot commented Jan 26, 2022 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 159b9da

+| ✅ 139 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

✅ Tests passed:

Run details

  • nf-core/tools version 2.2
  • Run at 2022-01-26 12:13:06

d4straub
d4straub approved these changes Jan 26, 2022
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Looks good to me!
I have only comments/suggestions/questions that are optional, so I approve it right away.

CHANGELOG.md Outdated Show resolved Hide resolved
workflows/ampliseq.nf Show resolved Hide resolved
modules/local/format_taxresults.nf
path(fastafile)
val(outfile)
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It would be sort of more obvious and functional when

ampliseq/bin/add_full_sequence_to_taxfile.py

Lines 35 to 39 in f1abc20

outfile = taxfile.replace("ASV_ITS_", "ASV_")
# Join taxonomy and full sequence, write to file
tax = tax.set_index('ASV_ID').join(seqs.set_index('id'), how='outer')
tax.to_csv(outfile, sep='\t',na_rep="", index_label="ASV_ID")

would actually use the value coming in here I think. But it works the way you are doing it right now I guess.

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It works, but you are right. Thanks for the suggestion!

@jtangrot jtangrot merged commit 6c5569d into nf-core:dev Jan 26, 2022
@jtangrot jtangrot deleted the addspecies_optional branch January 26, 2022 13:41
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@jtangrot @d4straub