ibern

A lot of bioinformatics code relies very heavily on pipes.

Don't underestimate American stupidity.

Couldn't agree more. You can't really speak about sonics in absolutist terms. Even so-called audiophiles can't agree on ideal sonics - is it a hyperclean recording with zero distortion and incredible dynamic range on CD, or is it the sound of tubes and tape on vinyl?

Their therapeutic area focus was far too broad. Going after "dozens of diseases" in parallel was a recipe for disaster. It takes a very specific understanding of your disease to translate genetic insight into a mechanistic, testable hypothesis.

The real value they tried to build was in pharma, which is much more lucrative than either of those. Their data is somewhat interesting but limited by the lack of rich phenotypic/clincial information paired with the genetics.

The advantage is that it's faster to prototype/write on the command line and usually ends up being less verbose (although potentially harder to read). It's easy to see what you're data is doing as you work with it and incrementally add pipes to new commands.

I like to use command line tools for for one-off tasks that I'm unlikely to repeat. If there's a task I know I'll need to repeat or is too cumbersome to do in a couple of lines, I'll reach for Python.

Here are some ways you could simplify some of the tasks in the article, saving on typing:

    cat data.csv | sed 's/"//g'

can be simplified by doing this instead:

    cat data.csv | tr d '"'

This awk command:

    cat sales.csv | awk -F',' '{print $1}' | sort | uniq

Can be replaced with a simpler (IMO) cut instead:

    cat sales.csv | cut -d , -f 1 | sort | uniq

When using head or tail like this:

    head -n 3

You don't need the -n:

    head -3

Also shout out to jq, xsv, and zsh (extended glob), all nice complements to the typical command line utils.

Right now I'd say it's in competition with Workflow Description Language (WDL), Nextflow, and maybe Snakemake.

CWL seems to be more popular than WDL, as far as I can tell, but Nextflow is probably more popular than both.