Closed johnbradley closed 3 years ago
@johnbradley, yeah this line calls for the genome reference which is something that can be stored in memory or in the path at the beginning..... I was thinking in something like GENOME=MT246667.fasta..... and then it should be called with $GENOME right?
@johnbradley, yeah this line calls for the genome reference which is something that can be stored in memory or in the path at the beginning..... I was thinking in something like GENOME=MT246667.fasta..... and then it should be called with $GENOME right?
That sounds like a good fix. Would you want to pass this in as an argument? Something like this:
./run-escape-variants.sh --genome=MT246667.fasta
yes, indeed! that would be a great argument. because also depending on the experiment. we can use a different genome reference.
One argument that would be nice to add at some point is a coverage thresholding parameter. You know... that file table.sort.tab is a table with a column that reports the percentage of the genome that is covered by at least one read. It would be nice to say that only mapped libraries with >90% coverage get their consensus sequence. But we can worry about this later since Nico is testing a new kit that may increase the percentage of genome coverage.
This issue has been fixed by #11
The pipeline has some duplicated hard coded values.
For example
MT246667
is in many locations such as:https://github.com/wodanaz/Assembling_viruses/blob/ebbb2bf0526d567a1bce766b6b32d8f236fd9f06/scripts/index-reference-genome.sh#L12
https://github.com/wodanaz/Assembling_viruses/blob/ebbb2bf0526d567a1bce766b6b32d8f236fd9f06/scripts/apply-bqsr.sh#L17