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Add in nf-validation for samplesheet #114

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edmundmiller opened this issue Jun 26, 2023 · 2 comments · Fixed by #117
Open

Add in nf-validation for samplesheet #114

edmundmiller opened this issue Jun 26, 2023 · 2 comments · Fixed by #117
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@edmundmiller
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enhancement New feature or request
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2.3.0

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@edmundmiller
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edmundmiller commented Jun 26, 2023 •
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Description of feature

Follow up to #113 to address the possible foot gun.
@edmundmiller edmundmiller added the enhancement New feature or request label Jun 26, 2023
@edmundmiller edmundmiller added this to the v2.2.0 milestone Jun 26, 2023
@edmundmiller edmundmiller self-assigned this Jun 26, 2023
@edmundmiller edmundmiller mentioned this issue Jun 26, 2023
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@edmundmiller edmundmiller linked a pull request Aug 25, 2023 that will close this issue
Use fromSamplesheet #117
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Need to validate that #113 is prevented

@Caffeinated-Code
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Hi @emiller88!

Ran into the same issue.

The nf-core also discusses this issue with the solution here for now:
https://github.com/nf-core/chipseq/issues/313

Turns out the naming convention in the sample sheet is throwing issues midway in the pipeline at samtools sort after UMI deduplication. Can we please try to catch this at the check_samplesheet.py level in this fix?

@edmundmiller edmundmiller modified the milestones: v2.2.0, 2.3.0 Feb 14, 2024
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Use fromSamplesheet nf-core/nascent
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