Samuel Lampa
Samuel Lampa
It is really annoying when runs are stopped because of existing temp folders, and one need to craft an rm command to delete them (which is also a bit dangerous)....
There are multiple situations where it makes sense to send a collection of file (paths) bundled together. Cases include: - Forward and reverse strand FastQ read files - A list...
@jonalv reported that output from the concatenator component are sometimes mixed up, where one row from one component is not finished until another one is written.
How to reproduce 1. Clone the SciPipe repo 2. `cd` into the repo folder 3. Check out the latest version, e.g. commit 0779cb0c04e98f0ae04d4af36dab7690658db54d 4. Run `go test .` Expected behaviour:...
Right now there is the [FileCombinator](https://pkg.go.dev/github.com/scipipe/scipipe/components#FileCombinator) and [ParamCombinator](https://pkg.go.dev/github.com/scipipe/scipipe/components#ParamCombinator) for producing combinations / "permutations" based on streams of either files or parameters. We either also need a combined component for boths...
A current shady spot in SciPipe is when needing to generate many sets of parameter values or file names to feed a downstream pipeline. This can be done to some...
It would be great with the ability to use "go to definition" inside Nextflow pipelines, especially for pipelines split up into many subworkflows and modules. Perhaps already possible via some...
Is there a configuration option to also highlight `.config` files? Otherwise, perhaps that would be great to add?
(I commented also [here](https://github.com/common-workflow-language/workflows/commit/84bfbb782d39f1e54c1f6d293d9dd9541468dbd0#commitcomment-17349629) about this.) This is relevant to the Picard sub-tools. I noticed that at least when intalling via apt-get on Ubuntu, you get a `picard-tools` script in...
This fixes #88