Hello, I've encountered an error trying to pass a pre-computed assembly to mag. I'm working with PacBio HiFi reads, pre-cleaned and assembled with Flye, on an AWS EC2 (AWS Linux 2023, x86_64). Here is the command I used:

nextflow run nf-core/mag -r 5.3.0 \
--input manifest.csv \
--assembly-input manifest-assembly.csv \ 
--run_busco false --run_checkm true \
--checkm_db /home/ec2-user/db/checkm \
--gtdb_db /home/ec2-user/db/gtdbtk/release220 \
--ancient_dna false \
--igenomes_base false \
-w <s3://mag-lr-test/work> \ 
--outdir <s3://mag-lr-test/out_results> \
-profile docker

The pipeline launches with this error:

WARN: The following invalid input values have been detected:

* --assemblyInput: manifest-assembly.csv

The pipeline runs but goes to the assembly step instead of skipping and going straight to binning. I have tried this with version 5.4.0 and 5.3.0 (shown) but end up with the same issue. I double checked my manifest and the --assembly-input flag seems to be correct, but no avail. Not sure what I'm doing wrong here but any help would be great! Thank you!

All I can say is

Can you try it with --assembly_input instead?

(makes 0 sense to me that it would... But that's the only thing I can think of atm)

It's Nextflow that does that automatic conversion, it's pretty annoying for nf-schema 😅

That is really nasty... And nf-schema can't tell Nextflow to 'not' somehow?

Nope, it's already happened when we read in the parameters. I thought we checked for it but seems you found an edge case

Ugh, but ok. Regardless thank you for the fast response @Nicolas Vannieuwkerke!

That did it! Minimap2 is executing now beer parrot

No worries! Glad I could help

Thank you both for your help, and thanks for the tip, did not know that about nf-schema