Closed johnbradley closed 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.
*.dedup.bam
bams.list
Right, rerunning the pipeline is not recommended unless the bams.list file is removed.
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 thebams.list
when the pipeline is rerun.