OpenGene / fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
MIT License
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Split interleaved output #551

Open Poshi opened 8 months ago

Poshi commented 8 months ago

I'm trying to get a splitted interleaved output for a pair end experiment, but I cannot find the proper command line. Is this even possible? I tried

$ fastp --in1 input_1.fastq.gz --in2 input_2.fastq.gz --stdout --split 2
ERROR: splitting mode cannot work with stdout mode

and

$ fastp --in1 input_1.fastq.gz --in2 input_2.fastq.gz --split 2 --out1 /tmp/test.fastq
ERROR: paired-end input, read1 output should be specified together with read2 output (--out2 needed)

But no luck so far. I also tried interleaving first and splitting later, but it doesn't work either:

$ fastp --in1 input_1.fastq.gz --in2 input_2.fastq.gz --stdout > /tmp/test.fastq
.
.
.
$ fastp --in1 /tmp/test.fastq --interleaved_in --out1 /tmp/test.split.fastq --split 2
ERROR: paired-end input, read1 output should be specified together with read2 output (--out2 needed)

I could also try to perform the split in the first place and then iterate over the several files to interleave them, but this is quite cumbersome.