Can tb-profiler collate include spoligotyping report ?

[ryobon-dev]

Hi,

tb-profiler collate is really helpful function in TBprofiler.
However, I noticed that it did not include spoligotyping report.
It would be helpful that you include spoligotyping report in tb-profiler collate.

Can you consider this ?

[jodyphelan]

Sure I can add this into the next version.

[jodyphelan]

Hi @ryobon-dev

This has now been added and will be included in the next bioconda release (v4.5.0)

[ryobon-dev]

Great !

When will you include it in the next bioconda release.
Can I expect to get it soon ?

Anyway, I eager to use it soon.

[jodyphelan]

Yes it should be ready today or tomorrow!

This is what collate looks like at the moment:

sample	main_lineage	sub_lineage	spoligotype	DR_type
por5A_illumina_bwa_freebayes_PE	lineage4	lineage4.3.4.2	777777607760400	MDR-TB
por5A_illumina_bwa_gatk_PE	lineage4	lineage4.3.4.2	777777607760400	MDR-TB
por5A_illumina_bwa_bcftools_PE	lineage4	lineage4.3.4.2	777777607760400	MDR-TB
por5A_illumina_bwa_pilon_PE	lineage4	lineage4.3.4.2	777777607760400	MDR-TB
por5A_illumina_bwa_lofreq_PE	lineage4	lineage4.3.4.2	777777607760400	MDR-TB
por5_vcf	lineage4	lineage4.3.4.2		MDR-TB

[jodyphelan]

Ok it should be available now on bioconda (v4.4.1)