GFAstats hangs with unrecognized action

[Mahesh Binzer-Panchal]

Bug report

When running gfastats with the input:

RVCP    MT192765.1

the tool shows the following error when instructions are separated by spaces:

unrecognized action RVCP    MT192765.1

and Segmentation faults when the instruction is separated by a tab. ( I can't replicate this anymore)

The input file is https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta

command run:

gfastats -k assembly.sak genome.fasta

Using the biocontainer quay.io/biocontainers/gfastats:1.3.5--hd03093a_0

Requests:

• Include SAK instructions must be tab separated on the instructions page and tool help
• Include which scale and units genome size should be on the README and help.

Additional context

I'm attempting to make a module for nf-core: nf-core/modules#2608

[Mahesh Binzer-Panchal]

Issue seems to be solved by using by using a tab to separate the instruction. Not sure how the seg fault occured.

[Giulio Formenti]

Ok thanks for reporting it. Will see if someone incurs in the same issue.