Clash of '-d' flag in cli commands

[Beatriz Vinhas]

Description

The command cg deliver ticket -t <ticket_id> -d <delivery_type> fails with error:

Try 'cg deliver ticket --help' for help.

Error: Missing option '-d' / '--delivery-type'. Choose from:
	balsamic,
	balsamic-qc,
	balsamic-umi,
	mip-dna,
	mip-rna,
	microsalt,
	fastq,
	mutant,
	rnafusion,
	taxprofiler,
	tomte

The error seems to happen because the option for --dry-run also allows for the abbreviated flag -d, which causes a clash with -d / --delivery-type.

Suggested solution

• Remove the abbreviation -d from the dry run option --dry-run

This can be closed when

There is no clash for the '-d' flag in cli commands.

Blocked by

If there are any blocking issues/prs/things in this or other repos. Please link to them.

[Vadym]

Muttacs process-solved is also affected ("-d", "--days-ago").

Could we use -dt for the delivery_type and -da for --days-ago? @beatrizsavinhas

Deliver ticket it's not part of the automation, and cg upload process-solved uses --days-ago

[Vadym]

Would you like to have a look @eliottBo?

[Beatriz Vinhas]

Muttacs process-solved is also affected ("-d", "--days-ago").

Could we use -dt for the delivery_type and -da for --days-ago? @beatrizsavinhas

Deliver ticket it's not part of the automation, and cg upload process-solved uses --days-ago

I guess we could, but I think there are other -d flags too in other commands. downsample is an example.

[Vadym]

I think I went through all of them, and for the rest of the options with -d (like --down-sampled), we don't have a dry-run, so they should not be affected

[EliottBo]

Yes I would like to take a look. Is it better to change the other flags that use now -d as a flag than to change the dry-run one?

[Henrik Stranneheim]

Yes I would like to take a look. Is it better to change the other flags that use now -d as a flag than to change the dry-run one?

Yes I think so. I prefer non standard Unix flag (i.e, not -v, -h) to have verbose names so they are mnemonic. For example: --delivery-type. These do not need a short flag because it can cause clashes and are hard to remember.