Small inconsistencies and bugs

[erikrikarddaniel]

Description of the bug

When running the dev version (20250127, i.e. after the Diamond thing), I find a couple of annoyances we should fix:

• One can't run with --help because it complains about --input not being present. I presume the help param is checked too late, i.e. after parsing of params. Probably came with a template update.
• I get this: WARN: Invalid config manifest attribute contributors``. I guess this is another template update thing. (Probably an old version of Nextflow at Dardel.)
• There are TODO-strings, at least in the ro-crate...json.
• "Badges" badly formatted and Zenodo citation missing in README.md
• We have a couple of unsupported param warnings:

WARN: The following invalid input values have been detected:

* --project: naiss2024-22-470
* --max_memory: 1.7 TB
* --max_cpus: 256
* --max_time: 7d
* --schema_ignore_params: genomes,input_paths,cluster-options,clusterOptions,project,validationSchemaIgnoreParams
* --validationSchemaIgnoreParams: genomes,input_paths,cluster-options,clusterOptions,project,schema_ignore_params
* --validation-schema-ignore-params: genomes,input_paths,cluster-options,clusterOptions,project,schema_ignore_params

Some of these are perhaps because of the pdc_kth config. And --project is perhaps not used by pdc_kth.

Command used and terminal output

Relevant files

No response

System information

No response

[erikrikarddaniel]

@danilodileo One point remains to be checked before we close this one: The badges, i.e. various icons in README.md.

[danilodileo]

I checked and we have all badges apart from the Citing one. Since we don't have a preprint out we can't solve this issue.

[erikrikarddaniel]

OK, so we have the Zenodo one? If so, just close this issue.

[danilodileo]

Yes, the Zenodo is there