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epi2me-labs / wf-bacterial-genomes

Small variant calling for haploid samples
https://labs.epi2me.io/
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Flye circular prediction #37

Closed VICTO160 closed 1 week ago

VICTO160 commented 5 months ago

Is your feature related to a problem?

no

Describe the solution you'd like

Can either the flye_stats.tsv file be saved in the output file, or the contigs be reported as circular/linear in the HTML file output.

Describe alternatives you've considered

Manually copying file out of intermediate subdirectories.

Additional context

No response

cjalder commented 5 months ago

@VICTO160 Thanks for raising this. Its a hotly requested feature so we'll be working on adding it to the next release!

angelovangel commented 4 months ago

Just publishing the flye_stats.tsv would be great.. I still dont understand why is this not published, as this is the point of the whole pipeline. In the meantime one can use

find work -type f -name *_flye_stats.tsv -exec cp "{}" . \;

to get them out of the work directory.

cjalder commented 1 week ago

Hi both - sorry for the delay. This should now be in the report in v1.4.1, with the flye stats tsv also being outputted