FASTP output naming breaks downstream processing #9589
Description
Have you checked the docs?
Description of the bug
FASTP output files for paired-end reads use "_1", "_2" rather than "_R1", "_R2". This failure to follow convention leads to bugs in downstream processing. E.g. in the scrnaseq pipeline, cellranger cannot process these files and throws an error as they don't match the expected naming scheme.
Command used and terminal output
Relevant files
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System information
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