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molikd / otb

Only The Best (Genome Assembly Tools)
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Possible issue with $BUSCO check in template.slurm files #60

Open dluecke opened 5 months ago

dluecke commented 5 months ago

In the SLURM templates the otb.sh submission is conditioned on whether BUSCO will be run, but that conditional statement is opposite in the otb.template.slurm ( if [[ -z "$BUSCO" ]] ) and otb.lite.template.slurm ( if [[ ! -z "$BUSCO" ]] )

In otb.template.slurm:

if [[ -z "$BUSCO" ]]; then
  ./otb.sh -n ${Assembly_Name} -f "$( echo ${Forward})" -r "$(echo ${Reverse})" -in "$(echo ${CCS})" -m ${HiFi_Type} -t ${Threads} ${Yahs} ${Busco} --polish_type ${Polish_Type} --runner ${Runner} -c -s
else
  ./otb.sh -n ${Assembly_Name} -f "$( echo ${Forward})" -r "$(echo ${Reverse})" -in "$(echo ${CCS})" -m ${HiFi_Type} -t ${Threads} ${Yahs} ${Busco} ${Busco_Location} ${Busco_DB} --polish_type ${Polish_Type} --runner ${Runner} -c -s
fi

In otb.lite.template.slurm:

if [[ ! -z "$BUSCO" ]]; then
  ./otb.sh --lite -n ${Assembly_Name}  -in "$(echo "${CCS}")" -m ${HiFi_Type} -t ${Threads} --runner ${Runner} -c -s
else
  ./otb.sh --lite -n ${Assembly_Name}  -in "$(echo ${CCS})" -m ${HiFi_Type} -t ${Threads} --runner ${Runner} ${Busco} ${Busco_Location} ${Busco_DB} -c -s
fi

I think both should look like the former.

Also the variables set in the script include $Busco but not $BUSCO. Unless $BUSCO is set elsewhere that's probably a typo as well.

molikd commented 1 month ago

Confirmed, also because busco work directory has changed, that needs to be added to otb.sh and template as well.