Add nag to cite the 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.

[apeltzer]

Could add this to the template, yeah, but the Zenodo DOI isn't automatically added (yet!) so having/reserving that would be really cool. x-ref #319 as this would be helpful

[ewels]

I think that @drpatelh has added functionality for this in the dsl2_template branch.

Not sure on the details of how it is implemented though...

tools/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/lib/Checks.groovy

Lines 67 to 76 in 5919f41

	// Citation string
	private static String citation(workflow) {
	return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
	"* The pipeline\n" +
	" https://doi.org/10.5281/zenodo.1400710\n\n" +
	"* The nf-core framework\n" +
	" https://dx.doi.org/10.1038/s41587-020-0439-x\n" +
	"* Software dependencies\n" +
	" https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
	}

[drpatelh]

Yes, its there! Will still need to update the Zenodo ID on first release and actually add citations to CITATIONS.md but other than that it will be printed every time a pipeline is run.