APPS-1271 Update improve manifest docs

[Gvaihir]

(fix) ExpertOptions.md - clarification of manifest inputs. Fixed example

[emiloslavsky]

some changes, a request for examples and some questions to improve my understanding of manifest mode.

[Gvaihir]

Thanks for the reviews/fixes @emiloslavsky

[Gvaihir]

@emiloslavsky latest changes incorporated. thanks!

[emiloslavsky]

missing ` otherwise LGTM

[Gvaihir]

@commandlinegirl - could you approve if my comments satisfy your request for changes? I tried to outdate them but it didn't work

[commandlinegirl]

Suggested change

	In extreme cases, running compiled workflows can fail due to DNAnexus platform limits on the total size of the input and
	output JSON documents of a job. An example is a task with many inputs/outputs that is called in scatter over a large collection.
	In such a case, you can enable manifest support at compile time with the `-useManifests` option.
	This option causes each generated applet or workflow to accept inputs as an array of manifests, and to produce outputs as a single manifest.
	In extreme cases, running compiled workflows can fail due to DNAnexus platform limits on the total size of the input and output JSON documents of a job. An example is a task with many inputs/outputs that is called in scatter over a large collection. In such a case, you can enable manifest support at compile time with the `-useManifests` option. This option causes each generated applet or workflow to accept inputs as an array of manifests, and to produce outputs as a single manifest.

It's a minor thing but it's easier to read (now and in the future) if there are no newlines introduced.

[commandlinegirl]

Here and below wherever the breakline is added.

[Gvaihir]

Actually, this new line here looks ugly to show the difference in versions. In the raw source it looks fine and there's no change in the rendered variant. But without this break line - the source looks like one stretched line and you have to scroll sidewise to read it. So I would really insist on having those break lines in the markdown docs from now on.

[Gvaihir]

This is how it looks now:

dxCompiler/doc/ExpertOptions.md

Line 1444 in 455de1d

In extreme cases, running compiled workflows can fail due to DNAnexus platform limits on the total size of the input and

This is how the rest of the doc looks without new lines:

dxCompiler/doc/ExpertOptions.md

Line 1296 in 455de1d

When calling a workflow with `dx run`, jobs and analyses launched by this workflow will have their temporary workspaces to store resources and intermediate outputs. By default, when a job or an analysis has transitioned to a terminal state (done, failed, or terminated), its temporary workspace will be destroyed by the system.

To me second example is harder to read compared to my version

[Gvaihir]

please click the links to actually see it in the raw .md

[commandlinegirl]

We don't want to inform the user of what the input_manifest___ is?

[Gvaihir]

It's not as simple. It does have this field, as well as a bunch of others, which I could not find the documentation for. APPS-1309 ticket should address that.

[commandlinegirl]

Gotcha. Thanks!