When starting an OTB run via otb.sh ... --yahs the pipeline doesn't reach scaffolding associated steps (egprocess yahs_faidx and process hicstuff) because the value params.scaffold = false isn't modified. otb.sh does not have a line to add the --scaffold flag to the RUN="nextflow run run.nf " string. Adding --scaffold ... -resume to the nextflow run command and resubmitting to SLURM allows the run to reach scaffolding and further steps.
An easy way to resolve this problem would be changing line 332 of otb.sh from
[ -n "$YAHS" ] && RUN+="--yahs "
to
[ -n "$YAHS" ] && RUN+="--scaffold --yahs "
molikd
commented
3 months ago
When starting an OTB run via
otb.sh ... --yahsthe pipeline doesn't reach scaffolding associated steps (egprocess yahs_faidxandprocess hicstuff) because the valueparams.scaffold = falseisn't modified.otb.shdoes not have a line to add the--scaffoldflag to theRUN="nextflow run run.nf "string. Adding--scaffold ... -resumeto thenextflow runcommand and resubmitting to SLURM allows the run to reach scaffolding and further steps.An easy way to resolve this problem would be changing line 332 of
otb.shfrom[ -n "$YAHS" ] && RUN+="--yahs "to[ -n "$YAHS" ] && RUN+="--scaffold --yahs "Thank you!