extract does not accept a gzipped sequence file

[donovan-h-parks]

GroopM extract does not work with a sequence file that is gzipped (e.g., groopm extract my_bins.gm my_scaffolds.fa.gz -o bins).

[wwood]

untested, but maybe this?

pigz -cd my_scaffolds.fa.gz |groopm extract my_bins.gm -o bins /dev/stdin

[minillinim]

Fixed