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please document the recursive behaviour of the --fastqs DIR, and fix misleading error message should this lead to duplicates #247

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plijnzaad opened this issue Jul 11, 2024 · 1 comment

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@plijnzaad
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I just spent three days debugging a 'feature' that is undocumented and unexpected: cellranger 'hunts' for samples recursively under the DIR specified by the --fastqs argument. The background to this is that I had to doctor some fastq files but keep the same name to be compatible with the rest of our infrastructure. So I did something like

cd /hpc/cache/fastq
mkdir orig
mv LX413* orig/
mv ~/tmp/subsampled/LX413* ./

just so I could use our launcher and database, yet keep the originals in cache. This behaviour is completely undocumented and what's worse, the resulting error message is misleading:

Duplicate FASTQs found between Sample LX413 in "/hpc/cache/fastq" and Sample LX413 in "/hpc/cache/fastq"

this should have been

Duplicate FASTQs found between Sample LX413 in "/hpc/cache/fastq" and Sample LX413 in "/hpc/cache/fastq/orig"

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Thank you for your interest in Cell Ranger. GitHub Issues are not monitored by our support team. Please e-mail [email protected] for support with Cell Ranger or visit our documentation site at https://www.10xgenomics.com/support/software/cell-ranger.

@github-actions github-actions bot closed this as not planned Won't fix, can't repro, duplicate, stale Jul 11, 2024
@github-actions github-actions bot locked and limited conversation to collaborators Jul 11, 2024
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