workflows

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It's a relatively common standard in the bioinformatics tools we wrap to not have any special handling for empty inputs or outputs (including headered files without content/alignments). These "empty" files...

a-frantz

Add trailing commas. Add blank lines between elements.

adthrasher

a-frantz

a-frantz

Some of our tasks allocate a large static amount of RAM that is often an over-allocation for many inputs. One example here: https://github.com/stjudecloud/workflows/blob/main/tools/ngsderive.wdl#L366

a-frantz

Major culprit here is HTSEQ: https://github.com/stjudecloud/workflows/blob/main/tools/htseq.wdl It has a pretty terrible sort algorithm and eats up resources when the input is position sorted. We've exposed the name sort option but...

a-frantz

See here: https://github.com/stjudecloud/workflows/blob/main/tools/fastqc.wdl#L59 The above may not work if `prefix` is messed with.

a-frantz

Expose more parameters of tools

1

In the early days of this repo we tended to only expose parameters we use. We've since gotten much better at exposing parameters as we add tools. But there are...

a-frantz

I think it's appropriate to default to gzipped inputs and that should be the standard we support. I don't see a need to go out of our way to support...

a-frantz

All of our workflows and (almost) all of our tasks assume that data is Paired-End. SE support would make our workflows and tools more accessible.

a-frantz