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Add SH information to sbdi export #448

Merged
merged 7 commits into from Jun 14, 2022
Merged

Add SH information to sbdi export #448

merged 7 commits into from Jun 14, 2022

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jtangrot
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@jtangrot jtangrot commented Jun 9, 2022

Modified SBDI-export scripts to add SH information, if available.
Input channels to SBDIEXPORT and SBDIEXPORTREANNOTATE are changed from DADA2_ADDSPECIES.out.tsv to ch_dada2_tax to capture the SH information. The tests I've done run as expected, but please let me know if you think this change will break anything.

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 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.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jun 9, 2022 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 536926c

+| ✅ 147 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-06-14 07:06:56

erikrikarddaniel
erikrikarddaniel approved these changes Jun 13, 2022
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@erikrikarddaniel erikrikarddaniel left a comment •
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Looks good, but needs pull from upstream it seems.

@jtangrot
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Looks good, but needs pull from upstream it seems.

Thanks!

@jtangrot jtangrot merged commit e1bdbfb into nf-core:dev Jun 14, 2022
@jtangrot jtangrot deleted the fix_sbdi branch June 14, 2022 09:18
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@jtangrot @erikrikarddaniel @d4straub