[-d topDir] argument is not passed correctly to -i argument for postprocessing

[Norbittner]

Describe the bug When running the juicer pipeline with the following command

./opt/scripts/juicer.sh -S final -D $(readlink -f opt) -z $(pwd)/opt/references/hg38.p13.fa.gz -d $(pwd)/L79851_Track-123454/ -p hg38 -t 32

it is not recognizing the location of the aligned files which should be passed to postprocessing.sh and giving the error

***! Error! Either inter.hic or inter_30.hic were not created

However these files were successfully created and when i run the postprocessing manually with

../opt/juicer/CPU/common/juicer_postprocessing.sh -j ../opt/juicer/CPU/common/juicer_tools -i ./aligned/inter_30.hic -g hg38 ../opt/juicer/CPU/common/juicer_postprocessing.sh -j ../opt/juicer/CPU/common/juicer_tools -i ./aligned/inter.hic -g hg38

everything works.

Expected behavior Juicer pipeline running from start to end.

Desktop (please complete the following information):

• OS: [openSUSE Leap 15.3]
• Version [Juicer 2.0]

Additional context Add any other context about the problem here.

[kellyliyichen]

Hi,

I think this is also the problem in check.sh. It seems that check.sh does not get the $outputdir parameter so it could not find inter.hic and inter_30.hic inside it and though out the error Either inter.hic or inter_30.hic were not created. Check for results

I found that in this line https://github.com/aidenlab/juicer/blob/c88f0893e96e7ed156cebc5e231578054f132c6c/CPU/juicer.sh#L763

it export $splitdir, so maybe it should also export $outputdir?