Enable multiple input file for forward/reverse about adapterremoval HOT 3 CLOSED

Hi Alexander,
I was actually thinking about something like --file1 fileX_R1 --file1 fileY_R1 --file1 fileZ_R1 --file2 fileX_R2 --file2 fileY_R2 --file2 fileZ_R2. But I think that your solution is not only neater, but should also be easier to add based on my existing argument-parser code, so I'll go with what you suggest.

I hope to be able to work on this next week.

Cheers,
Mikkel

from adapterremoval.

Sounds good - no worries about the timing though!

from adapterremoval.

Support for multiple input files is now part of AdapterRemoval v2.2.1.

Based on your suggestion, the files are simply specified one after each other following the --file1 or --file2 option:

$ AdapterRemoval --file1 reads_1a.fq reads_1b.fq reads_1c.fq
$ AdapterRemoval --file1 reads_1a.fq reads_1b.fq reads_1c.fq --file2 reads_2a.fq reads_2b.fq reads_2c.fq

It should work entirely transparently (regardless of compression or lack thereof), but just let me know if you run into any issues.

Cheers,
Mikkel

from adapterremoval.