This code is associated with the paper from Crombie et al., "Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations". eLife, 2019. http://dx.doi.org/10.7554/eLife.50465

noaa-nf

Nextflow pipeline to pull weather data from NOAA weather stations around the world by GPS coordinates. Specified for Andersen Lab looking at weather surrounding date of isolation of C. elegans isotypes.

Requirements

Requires several R packages including "tidyverse", "geonames", "lubridate", "geosphere", and "stationaRy".

install.packages(c("tidyverse", "geonames", "lubridate", "geosphere", "devtools"))
devtools::install_github("rich-iannone/stationaRy")

Also requires nextflow installation. Check out this help page for more info.

wget -qO- https://get.nextflow.io | bash

Usage

nextflow run AndersenLab/noaa-nf --in='infile.csv'

Input

Input file is a .csv file containing columns isotype, latitude, longitude, and isolation_date. The isolation date should be in YYYY-MM-DD format.

isotype	latitude	longitude	isolation_date
AB1	-34.93	138.59	1983/01/01
CB4856	21.33	-157.86	1972/08/01
...	...	...	...
QX1211	37.7502	-122.433	2007/11/26

Optional Parameters

params	default	options	explanation
in	NA	name of input file	name of input file, required
months	3	Any number	Number of months surrounding date to collect weather data for
important_trait	NULL	Any one trait (listed below)	Chooses closest weather station to GPS coordinate that has sufficient data for this trait
events	10	Any number	keeps weather stations with at least events records per month
out	date	name of output file	name of output file

Example with options

nextflow run AndersenLab/noaa-nf --in='input.csv' --months='12' --events='100' --out='example_test'

Traits

Default traits

By default, the stationaRy package downloads 8 weather traits:

trait	description
wd	The angle of wind direction, measured in a clockwise direction, between true north and the direction from which the wind is blowing.
ws	Wind speed in meters per second
ceil_hgt	The height above ground level of the lowest clould cover or other obscuring phenomena amounting to at least 5/8 sky coverate. Measured in meters.
temp	Air temperature measured in degrees Celsius.
dew_point	The temperature in degrees Celsius to which a given parcel of air must be cooled at constant pressure and water vapor content in order for saturation to occur.
atmos_pres	The air pressure in hectopascals relative to Mean Sea Level (MSL).
rh	Relative humidity, measured as a percentage, as calculated using the August-Roche-Magnus approximation.
precip	Liquid precipitation, hourly, in inches.