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FischbachLab / nf-bacannot

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
https://bacannot.readthedocs.io/en/latest/
GNU General Public License v3.0
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Reports in one excel file #2

Open wing2250 opened 1 year ago

wing2250 commented 1 year ago

Currently, reports are in one folder, which is very helpful, but there are 4 files (report_general.html, report_MGEs.html, report_resistance.html, report_virulence.html) separately and I found myself downloading .csv files from individual links.

It would be really helpful if there is a merged report excel file with 4 tabs (general, MGEs, resistance, and virulence). It would be even better if the report title is "id_report".

image

@sunitj

sunitj commented 1 year ago

All outputs are listed as tables in the gffs folder. Exmple:

$ aws s3 ls s3://genomics-workflow-core/Results/Bacannot/MRSA/20221102/Staphylococcus_aureus_BDH17/gffs/
2022-11-02 16:29:42          0 
2022-11-02 16:29:43     741268 Staphylococcus_aureus_BDH17.gff
2022-11-02 16:29:43       1937 ices_iceberg.gff
2022-11-02 16:29:43      43784 prophages_phast.gff
2022-11-02 16:29:42       8906 resistance_amrfinderplus.gff
2022-11-02 16:29:43       9054 resistance_card.gff
2022-11-02 16:29:43       3376 transposable_elements_digis.gff
2022-11-02 16:29:43      22416 virulence_vfdb.gff
2022-11-02 16:29:42      12300 virulence_victors.gff

When you view the reports, it's showing you a cleaner version of these tables. If you wish I can write some scripts/notebooks to combine these for you, but we should talk more about what you'd like to see in the combined table. Maybe there is too much here and you'd like me to clean it up a bit..