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log.Rmd
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---
title: "Untitled"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
# Date:
clipr::write_clip(paste0('## ', format(Sys.time(), "%F (%A %B %e)\n\n")))
```
## 2022-03-29 (Tuesday March 29)
You can build just certain steps with something like:
`nextstrain build . export -f`
## 2022-02-16 (Wednesday February 16)
Can add a description file with arbitrary md/html with `export` option `--description`.
Can include images with `cat(sprintf("<img src=\"%s\" />\n", knitr::image_uri("test.jpeg")))` and other `knitr` tools II expect
## 2022-02-15 (Tuesday Feburary 15)
Looking for why samples are being filtered out.
Happens at `refine` step, due to the option `--clock-filter-iqd`.
Increasing the value stops the samples from being removed, but removing the option causes an error.
## 2021-12-16 (Thursday December 16)
Got it working yesterday.
Problem with overlapping ORFs
Nik says:
Zach, check if you can have overlapping ORFs as in nextstrain following this genome annotation:
Fig. 2
See: https://www.sciencedirect.com/science/article/pii/S0882401018305953?via%3Dihub