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Detect and warn if samples files with I1 / I2 FASTQ files are included #283

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pansapiens opened this issue Jan 18, 2024 · 1 comment
Open

Detect and warn if samples files with I1 / I2 FASTQ files are included #283

pansapiens opened this issue Jan 18, 2024 · 1 comment
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Occasionally sequencing providers return I1 and I2 FASTQ files (index and/or UMIs) along with the typical paired end R1/R2 files.
While some Laxy pipelines may accept these, the current nf-core/rnaseq pipeline does not.

For nf-core/rnaseq (and maybe others), if _I1_ or _I2_ is detected in the filename, show a prominent warning that these are likely not the files you should be using. Possibly with a "I'm sure, go ahead" checkbox that must be ticked to continue.
@pansapiens pansapiens self-assigned this Jan 18, 2024
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Partially addressed for one pipeline with commit 5dbdd2c - covering the case where I1 and I2 files are inside a tarball and the user has no opportunity in the UI to exclude them.

@github-project-automation github-project-automation bot moved this to To do in Laxy Aug 28, 2024
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