--mlst flag is not being passed on to mlst call

tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

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Closed andersgs closed 4 years ago

andersgs commented 5 years ago

It seems --mlst flag is not being passed on to mlst call.

nullarbor.pl --name Test --ref Bpseudo_M1.gbk --input input.txt --outdir nullarbor --mlst bpseudomallei --force

...
MLST := mlst
...
mlst.tab : $(FASTAREF) $(CONTIGS)
        mlst $^ > $@

tseemann commented 5 years ago

You are right... this could be tricky due to the static nature of my new Makefile.

tseemann commented 4 years ago

This also uncovered another bug where i define MLST := mlst ... but don't use it!