Diogo Silva

I third that!

> (short | long | short + long) unicycler (bandage | quast) @sjackman I'm not completely sure how this example would work but I'm trying to wrap my head around...

Hmm, in that case the parser would repeat the `C` component for each lane, under the hood, is that it?

The `secondary_inputs` process directive has been [deprecated in v1.2.1](https://flowcraft.readthedocs.io/en/latest/dev/create_process.html#secondary-inputs). Secondary inputs for a component can be provided via the [`parameters` directive](https://flowcraft.readthedocs.io/en/latest/dev/create_process.html#parameters). These parameters can be used in the nextflow template...

Right, so we can solve those shortcoming but we'll need to make some additions to flowcraft, some of which we already wanted to do for some time: - Add new...

Hmm, yes the problem of simplifying the pipeline orchestration with a single raw string is that you also don't have many simple options to build it. Changing to the syntax...

Just to follow up, the --fastq parameter syntax is a glob pattern that groups pairs of FastQ files in a single nextflow channel emission. It basically feeds into the `fromFilePairs`...

I agree with updating the error message. However, as you stated, it should be fine both ways but it seems to be a limitation of the nextflow channel. In the...

As discussed in #62, we would like to support both single and paired end reads in the future. I would prefer a solution that avoids multiplying the components by each...

I agree that this is something that needs to be addressed and added to flowcraft. Not only the ability to provide extra inputs, but also to specify different parameters for...