Add nag to cite pipeline in summary

[olgabot]

e.g. from khmer

|| This is the script load-graph.py in khmer.
|| You are running khmer version 2.1.2
|| You are also using screed version 1.0
||
|| If you use this script in a publication, please cite EACH of the following:
||
||   * MR Crusoe et al., 2015. http://dx.doi.org/10.12688/f1000research.6924.1
||   * J Pell et al., http://dx.doi.org/10.1073/pnas.1121464109
||   * A. Döring et al. http://dx.doi.org:80/10.1186/1471-2105-9-11
||
|| Please see http://khmer.readthedocs.io/en/latest/citations.html for details.

Same as nf-core/tools#382 -- could be tried out in this repo first

[apeltzer]

Yeah, should contain the Zenodo DOI I guess 👍

[apeltzer]

@nf-core/core Any further thoughts on this? Having a comment/citation in the README.md of each pipeline is a good idea and already adhered by some pipelines. However, if I understand @olgabot here correctly, the suggestion is to also have that in the actual pipeline and output something on the log.info ... when running the pipeline. I think it is a good idea, but that is something that is nowhere present so far...

[drpatelh]

I guess this is something we could think about when we have machine readable citation format implemented such as suggested here:
nf-core/tools#361

One of the biggest downsides of outputting it in a log.info would be that it could be a very very long list of citations and shouldnt really be mixed in with the pipeline parameters in my opinion...maybe having another parameter such as --cite where we could exclusively output this would be better?

[ewels]

shouldn't really be mixed in with the pipeline parameters in my opinion...

Agreed, but you could have it at the end of execution instead.. And in the email / pipeline report. But yeah, could get spammy. Maybe just reference the file that we bundle that has the citations? Then it's always the same length.

Regarding --cite, x-ref nf-core/tools#236 where I suggested basically this but for the command line helper tool.

[olgabot]

I like the idea of putting it in the pipeline report or at the very end as a reminder. People are lazy and won't remember to use the --cite command when they need to cite it, so I believe a spammy nag is necessary.

[drpatelh]

Fixed in #487

[drpatelh]

This will be printed at the end of the summary log info when the pipeline starts up and also when --help is specified. Will add this to the pipeline template when we port the DSL2 changes across.