Question: How to run EVALUATE_ASSEMBLY process without the 'assemble' step

[gbdias]

Now that the assembly evaluation is included in the 'assemble' workflow step, how do I evaluate an assembly produced outside of the pipeline?

I can skip assembly by using the steps parameter:

params {
    steps              = 'inspect,preprocess,screen'
}

But that skips evaluation as well.

[mahesh-panchal]

So as of commit https://github.com/NBISweden/Earth-Biogenome-Project-pilot/commit/5b9171f2df3cf7cc9c810c6ad691b79f88ff72c0 there's a few steps at the moment to make it work.

• You need to include stage: raw in the assembly input because of L125 in main.nf.
• You need to disable HIFIASM using a custom config so the workflow doesn't run on the assembler on the reads.

Your input file should look like:

sample:
  name: Species name
assembly:
  - assembler: hifiasm
    stage: raw
    id: uuid
    pri_fasta: /path/to/primary_asm.fasta
    alt_fasta: /path/to/alternate_asm.fasta
    pri_gfa: /path/to/primary_asm.gfa
    alt_gfa: /path/to/alternate_asm.gfa
  - assembler: ipa
    stage: raw
    id: uuid
    pri_fasta: /path/to/primary_asm.fasta
    alt_fasta: /path/to/alternate_asm.fasta
hifi:
  - reads: /path/to/reads

where uuid is some unique ID. and your custom config should look like:

process {
    withName: 'HIFIASM' {
        ext.when = false
    }
}

Do the same for MITOHIFI_FINDMITOREFERENCE too if you don't want that to run either. That should run only the evaluation tools then during the assemble stage.

Note this is just a fix and I'll make proper support once I'm back from holiday.

[gbdias]

thanks!