replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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new pangolin table columns #260

Closed replikation closed 5 months ago

replikation commented 5 months ago

current pangolin output table (conflict removed):

taxon,lineage,SH-alrt,UFbootstrap,lineages_version,status,note

needs adjustments in the workflow

old columns for reference:

{ grep "taxon," || exit 1; }
{ grep ",lineage," || exit 1; }
{ grep ",conflict," || exit 1; }
{ grep ",scorpio_call," || exit 1; }
{ grep ",scorpio_conflict," || exit 1; }
{ grep ",pangolin_version," || exit 1; }
{ grep ",scorpio_version," || exit 1; }
{ grep ",constellation_version," || exit 1; }
{ grep ",version," || exit 1; }
{ grep ",qc_status," || exit 1; }
{ grep ",qc_notes," || exit 1; }
replikation commented 5 months ago

and a new pangolin container update to avoid version conflicts