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Segemehl update #123

Merged
merged 2 commits into from
May 30, 2024
Merged

Segemehl update #123

merged 2 commits into from
May 30, 2024

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nictru
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@nictru nictru commented May 30, 2024

#122 introduced a bug with segemehl. The SEGEMEHL_ALIGN process originally had a single output channel containing a list of all output files. This was manageable before #122 because a specific process called SEGEMEHL_FILTER handled this list. In #122, we switched to the nf-core GAWK module for unification (and common filtering of the unified files afterward).
The GAWK/UNIFY module then used all files from the list output of SEGEMEHL_ALIGN as input. This was problematic since not all files followed the expected input format; thus, the output of UNIFY was partially binary.

The SEGEMEHL_ALIGN process was updated via a modules PR.
This PR integrates this update into the pipeline (other nf-core modules were also updated).

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github-actions bot commented May 30, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b81a30a

+| ✅ 226 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-30 12:23:45

JoseEspinosa
JoseEspinosa approved these changes May 30, 2024
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LGTM 🚀

@nictru nictru merged commit 0e9cce3 into dev May 30, 2024
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@nictru nictru deleted the segemehl-update branch May 30, 2024 13:00
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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