how to use pipe lines for kneaddata

[Ming Liao]

Hello, there

I have tested the following two commands, but failed. Is it possible for kneandata to handle this case?

zcat ./demo.fastq.gz | ~/.local/bin/kneaddata  --input  --reference-db ~/kneaddata_v0.5.1/db/Homo_sapiens_Bowtie2_v0.1 --output ./demo

The error is : kneaddata: error: argument -i/--input: expected one argument

~/.local/bin/kneaddata  --input <(zcat ./demo.fastq.gz)> --reference-db ~/kneaddata_v0.5.1/db/Homo_sapiens_Bowtie2_v0.1 --output ./demo

The erro is: kneaddata: error: unrecognized arguments:

What about using pipe lines for the paired-end data?

 kneaddata --input seq1.fastq --input seq2.fastq -db $DATABASE --output kneaddata_output`

Thanks

[Andy Shi]

Hi Ming, 

KneadData can directly handle gzipped files, so you can simply pass the demo.fastq.gz file to the input parameters.

You can just use

~/.local/bin/kneaddata  --input ./demo.fastq.gz --reference-db ~/kneaddata_v0.5.1/db/Homo_sapiens_Bowtie2_v0.1 --output ./demo