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Devin McCabe dpmccabe

  • Broad Institute of MIT and Harvard
  • Cambridge, MA
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@pryce-turner
pryce-turner / filebased_wf.md
Last active February 21, 2024 20:29
Processing Files with Dynamic Container Tasks in Flyte

Processing Files with Dynamic Container Tasks in Flyte

Motivation

I'm still very new to Flyte but it's quickly becoming one of my favorite tools. Between the modern architectural decisions and a welcoming and extremely helpful community, what's not to love?

Some of the abstractions however, do require a slight shift in assumptions compared to more localized workflow frameworks. Additionally, while the documentation is excellent at explaining Flyte's different features in isolation, there aren't as many posts on how they work together like there are for more established projects. This short piece is my attempt to capture my journey so far with a rather specific usecase that ties together a number of notable features. This is mostly to solidify my own understanding, but hopefully also a way to pay forward all the wonderful support I've received from the team.

Setup

  • Everything you need to run the code below is captured in the [Envi
@pimentel
pimentel / head.list.R
Last active June 27, 2018 03:09
Slightly more sane head() for lists in R
catDf <- data.frame(meow = rnorm(100), purr = rpois(100, 3))
aList <- list(aVector = 1:20, aDf = catDf, anotherList = list(1:200, 1:20))
# annoying as hell, right?
head(aList)
#' Return the first or last part of a list
#'
#' Returns the first or last part of a list. Instead of returning the first
#' n entries as the standard head() does, it attempts to call head()
@davetang
davetang / psl_to_bed_best_score.pl
Last active April 9, 2021 13:55
A more documented version of my psl_to_bed_best_score.pl script at http://davetang.org/wiki/tiki-index.php?page=Blat.
#!/usr/bin/env perl
use strict;
use warnings;
=head1 NAME
This scripts converts a psl file into a bed file written by Dave Tang.
=head1 SYNOPSIS