Added skip_citation_process flag to skip processing citation.md

[soichih]

Changes proposed in this pull request

This PR workarounds the issue of pandoc running out of vmem at the end of the fmriprep pipeline which then terminates the workflow on our HPC environement. #1870

Here is Neurostart discussion about this issue.

https://neurostars.org/t/large-virtual-memory-allocations-in-fmriprep-on-pbs-system/4665/8

Our workflow doesn't just run a single fmriprep, so if fmriprep fails at the end, it will kill the entire workflow. For us, it's important that fmriprep survives the post-processing. The memory issue with pando has been a known issue since 2016 according to this thread (jgm/pandoc#3169) ..

[welcome]

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[effigies]

Thanks. This should be moved to a different argument group.

I also wonder if there's a clearer name, but my brain isn't coming up with anything better. Something about "process" feels vague, and once it exists, it'll be annoying to change. So in case someone has a better idea, now would be a good time to change it.

[effigies]

Suggested change

	g_bids.add_argument('--skip_citation_process', '--skip-citation-process', action='store_true',
	g_bids.add_argument('--skip-citation-process', action='store_true',

Usually the _ one is there for backwards compatibility with old submission scripts. - is preferred, so we can use it on new options.

And this should go in g_perfm, not g_bids.

[soichih]

I will update the PR. Testing the update now.

[faskowit]

could 'skip-pandoc' or 'no-pandoc' be a more direct/intuitive flag name? Given the brief help text, I think it would still be pretty clear to users.

[emdupre]

could 'skip-pandoc' or 'no-pandoc' be a more direct/intuitive flag name?

I'm hesitant to mention pandoc in the argument, since I imagine a decent number of users won't be familiar with it.

What about --md-only-boilerplate ?

[pep8speaks]

Hello @soichih! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2019-11-24 21:50:23 UTC

[effigies]

LGTM. Any further comments?