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OpenGene / fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
MIT License
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Use with fifo? #571

Open GregTD42 opened 2 months ago

GregTD42 commented 2 months ago

I would like to use fastp with input coming over a fifo. Since you're a single pass tool, it appears this should work. But no matter how I try to set things up, I get

[2024-07-15T17:46:51-0500] [ERROR] [fastp_report.sh]    
fastp_report.sh stopped at line 170. 
REASON=Input read 1 file sample.L.fifo.fastq is empty or does not exist.

Should this in fact work?

sfchen commented 2 months ago

what's your command?

GregTD42 commented 2 months ago

fastp -i "$Input1Path" -I "$Input2Path" -w 6 -Q -A --overrepresentation_analysis >&2

The two Input?Path are fifos

GregTD42 commented 2 months ago 
leftFifo="sample.L.fifo.fastq"
rightFifo="sample.R.fifo.fastq"
mkfifo "$leftFifo"
mkfifo "$rightFifo"
zcat sample_1.fastq.gz > "$leftFifo" &
zcat sample_3.fastq.gz > "$rightFifo" &
Input1Path="$leftFifo"
Input2Path="$rightFifo"

In case that's what you were asking