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jajclement / hotSSDS

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Bedtools error in makeSSMultiQCReport_nextFlow.pl is not handled properly #10

Open andpet0101 opened 1 year ago

andpet0101 commented 1 year ago

The script makeSSMultiQCReport_nextFlow.pl calls bedtools to get the number of reads in known hotspots. However, if bedtools fails for some reason (e.g. not enough memory), the script itself does not fail. This will result in incorrect numbers (basically zero reads in hotspots). The script should check the return value of bedtools and fail if needed.

Such checks might also be necessary for other scripts/parts of the code.

paulineauffret commented 1 year ago

Hi, thank you for spotting that ! We are currently in the process of making major changes in terms of portability, and we wil also take into account the problems your raised in the issues. I'll let you know when the modifications are done and merge into master.

andpet0101 commented 1 year ago

Glad to hear!

Btw for the many bash scripts in the pipeline, I would suggest to include set -ef -o pipefail at the beginning (https://www.nextflow.io/docs/edge/process.html, script). That should cause the pipeline on most of the bash errors.