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Lint fastqs before and during preprocessing #7123

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pinin4fjords merged 10 commits into from
Dec 2, 2024
Merged

Lint fastqs before and during preprocessing #7123

pinin4fjords merged 10 commits into from
Dec 2, 2024

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@pinin4fjords pinin4fjords commented Nov 29, 2024

Adds a lint check at every step during preprocessing. FQ_LINT will fail, and does not return fastqs, so I just do a dummy join to make sure things don't go to other processes at

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@pinin4fjords pinin4fjords mentioned this pull request Nov 29, 2024
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maxulysse
maxulysse reviewed Dec 2, 2024
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@pinin4fjords pinin4fjords added this pull request to the merge queue Dec 2, 2024
Merged via the queue into master with commit 34774b3 Dec 2, 2024
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@pinin4fjords pinin4fjords deleted the fq_preprocess_lint branch December 2, 2024 15:57
@pinin4fjords pinin4fjords mentioned this pull request Dec 2, 2024
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LouisLeNezet pushed a commit to LouisLeNezet/modules that referenced this pull request Dec 4, 2024
@pinin4fjords @maxulysse
Lint fastqs before and during preprocessing (nf-core#7123)
412f88e 
* Lint fastqs before and during preprocessing

* Add lint_log to snaps

* put back file removed in error

* Update snap

* Fix tests

* Linting snapshots to md5

* Update subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf

Co-authored-by: Maxime U Garcia <[email protected]>

* Update swf meta.yml

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Co-authored-by: Maxime U Garcia <[email protected]>
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@maxulysse maxulysse maxulysse approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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