Open dluecke opened 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" ]] )
if [[ -z "$BUSCO" ]]
if [[ ! -z "$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 $BUSCO is set elsewhere that's probably a typo as well.
Confirmed, also because busco work directory has changed, that needs to be added to otb.sh and template as well.
In the SLURM templates the otb.sh submission is conditioned on whether BUSCO will be run, but that conditional statement is opposite in the otb.template.slurm (
if [[ -z "$BUSCO" ]]
) and otb.lite.template.slurm (if [[ ! -z "$BUSCO" ]]
)In otb.template.slurm:
In otb.lite.template.slurm:
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.