Open audy opened 3 weeks ago
Hi @audy
Thanks for the report, ugh this comes up so many times with Prokka.
Indeed, in other pipelines were we use this I've added a flag to turn this on. Probably simplest to do the same here. Will get to this ASAP.
Otherwise as a workaround until this is implemented, you can manually add this to a custom config file:
add to e.g. custom.conf
process {
withName: PROKKA {
ext.args = "--metagenome --compliant --centre-name something"
publishDir = [
path: { "${params.outdir}/Annotation/Prokka/${meta.assembler}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
And supply the file to your nextflow run command with -c custom.conf
.
I also don't know the exact effects will be, my main fear would be that the trimmed contigs name mean they might not be able to be associated with other output, but I guess that's up to the user. I don't think ti'll break the pipeline per se as the Prokka output files are not used elsewhere as far as I know.
Hi, I ran into this issue as well, and I used the suggest addition to my config file. I do get an error however.
This is what I added:
withName: PROKKA {
ext.args = "--metagenome --compliant --centre-name NVI"
publishDir = [
path: { "${params.outdir}/Annotation/Prokka/${meta.assembler}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
Which is similar to the suggestion, When I run the pipeline I get this error:
ERROR ~ Unknown config attribute `process.withName:PROKKA.params.publish_dir_mode` -- check config file: /cluster/projects/nn10070k/projects/phagedrive/pd_data_control/mag_asm_set-ups/run_20240726/saga_mag.simple.config
-- Check '.nextflow.log' file for details
Would it help to remove the publishDir from the config set-up?
YEs, please try that and have just ext.args
Hi, I needed to change the settings for PROKKA a little bit, because --centre-name
was not right. it needed to be --centre
.
The bit I added was:
withName: PROKKA {
ext.args = "--metagenome --compliant --centre NVI"
}
and it seems to be running now.
Yep that solved the issue. for me
Glad to know it works with that, yes we can add an option wiht that flag!
Description of the bug
I am running nf-core/mag 3.0.3 on a sample (ERR4303137) and it fails during the Prokka step.
This looks like it might be a simple fix (adding
--compliant --centre-name something
) but I'm not sure what the downstream effects will be.Command used and terminal output
Terminal output:
(click to expand)
Relevant files
No response
System information