Updating handling of `<pipeline directory>` in `nf-core`

[ErikDanielsson]

As was discussed on slack it would be good to not have to specify the pipeline directory as the current working directory on the different subcommands of nf-core The suggestion is therefore to specify pipeline directory with --dir <pipeline directory> with current working directory as default, instead of as <command> <pipeline directory>

[ewels]

Yup, I think that this would be great 👍

Will probably need a little testing / refining of what happens if the cwd is not a pipeline directory. Just to make sure that annoying stuff doesn't happen if people run the commands when accidentally in a subfolder etc. I was half wondering about traversing up the file tree to try to find a pipeline in this case, but I think it's probably overkill and easier / safer to just exit nicely.