Update file examples

[dorien-er]

Changelog

Make sure all arguments with type: file have a correct example attached.

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[DriesSchaumont]

Could you alway use a YAML list please?

input.bam, input.sam, input.cram

becomes

["input.bam", "input.sam", "input.cram"]

[dorien-er]

Could you alway use a YAML list please?

input.bam, input.sam, input.cram

becomes

["input.bam", "input.sam", "input.cram"]

This results in parsing issues, when we don't set multiple: true

[dorien-er]

Could you alway use a YAML list please?

input.bam, input.sam, input.cram

becomes

["input.bam", "input.sam", "input.cram"]

This results in parsing issues, when we don't set multiple: true

Let's discuss offline... May have to rethink the approach for parsing examples to show on VH from the configs