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View Code? Open in Web Editor NEWNextflow script for processing WGS data
Nextflow script for processing WGS data
A snp table similar to those produced by snippy would be a useful additional output.
This will first require clusters to be defined, so is a long term goal.
Perhaps this can be done by identification of closest SNP pattern?
Collect folder name from $PWD?
Need to filter kraken/bracken output so that presence of M.bovis in the sample is recognised and flagged. This should be added to the output csv file
The internationally recognized names for spoligotypes are available here: https://www.mbovis.org/
Need to change consensus calling so that when there is no data the reference sequence is not the output generated by default
Error code suggests that its linked to an issue in bcftools where two variants are overlapping. See samtools/bcftools#888. Fix available in latest bcftools commit, but not yet in a full release.
Add some more useful information!
Samples are not assigned to WGS clusters when cultures are contaminated. Can kraken be used to filter out contaminants before mapping/cluster assignment?
Use latest version of trimmomatic
Some spaces need to be converted to tabs so that columns are displayed correctly
Suggest run kraken on samples that do not give expected result
Updated reference genbank file leads to error in SNPfiltAnnot process:
AttributeError: 'CompoundLocation' object has no attribute '_start'
The python script for snp filtering needs to be changed to accept stdin, so that the uncompressed vcf can be piped in rather than written to disk
Currently if WGS cluster is not assigned, either bTB or LowCoverage is output. By using the data captured on %mapped and number of reads, it should be possible to determine if the sample should be repeated.
This part of the process needs work, both on the nextflow pipeline and the underlying python script to run correctly
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