Use with fifo?
GregTD42 opened this issue · 3 comments
GregTD42 commented
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
what's your command?
GregTD42 commented
fastp -i "$Input1Path" -I "$Input2Path" -w 6 -Q -A --overrepresentation_analysis >&2
The two Input?Path are fifos
GregTD42 commented
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