So I'm trapped 🙃 Is this a bug? Or do I need more any escapes? Any advice?

Is there not also a quotation error in the

nextflow_schema.json

? Is the closing

'

missing? 🤔

That's to getting back to me @Julian Flesch! I will double check everything this weekend at some point (lots of kids activities), the missing

'

that might be in the PR atm is because I tried just letting tools

schema build

reformat it (and it removes it automatically). I probably forgot to putit back What do you mean by moving the

--param-string

bit? to wheverever it is used?

I mean the pipeline param would just hold the value part:

# ADAPTED nextflow_schema.json
...
"sourmash_build_dna_options": {
                    "type": "string",
                    "default": "scaled=1000,k=31,noabund",  <<< THIS CHANGED
                    "fa_icon": "fas fa-users-cog",
                    "description": "Specify parameters given to sourmash sketch dna.",
...

And whereever the value is used you explicitly add back the "--param-string" use this you do:

# e.g. ADAPTED conf/modules.config:
ext.args = "dna --param-string ${params.sourmash_build_dna_options}"

Uuuhh well @Julian Flesch you were completely right - indeed the original JSON schema WAS missing the escapes... and for a long time (as i see it in

main

) 🙈 , and I guess tools got better at checking for mismatches 😬 . So indeed, no change needed from tools end, and we can ignore this! Thank you for looking with a clear mind on my behalf 😆

yeah seems fragile and maybe worth refactoring at some point

That would involve changing the upstream tool 🤣 We could I guess replace the per tool options parameters with 1:1, but the. With sourmash it would be n² things we have to add....