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wodanaz / Assembling_viruses

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Support rerunning the pipeline #8

Closed johnbradley closed 3 years ago

johnbradley commented 3 years ago

Currently rerunning the pipeline has issues due to how we find files. For example the code looks for all files named bam:

https://github.com/wodanaz/Assembling_viruses/blob/ebbb2bf0526d567a1bce766b6b32d8f236fd9f06/scripts/escape-variants-pipeline.sh#L52

Subsequent commands create *.dedup.bam files which get accidentally added to the bams.list when the pipeline is rerun.

wodanaz commented 3 years ago

Right, rerunning the pipeline is not recommended unless the bams.list file is removed.