HiCUP: pipeline for mapping and processing Hi-C data. - Steven W. Wingett; Philip Ewels; Mayra Furlan-Magaril; Takashi Nagano; Stefan Schoenfelder; Peter Fraser; Simon Andrews (F1000Research, 2015)

MultiQC: summarize analysis results for multiple tools and samples in a single report. - Philip Ewels; Måns Magnusson; Sverker Lundin; Max Käller (Bioinform., 2016)

Cluster Flow: A user-friendly bioinformatics workflow tool. - Philip Ewels; Felix Krueger; Max Käller; Simon R. Andrews (F1000Research, 2016)

Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants. - Maxime Garcia; Szilveszter Juhos; Malin Larsson; Páll Ísólfur Ólason; Marcel Martin; Jesper Eisfeldt; Sebastian DiLorenzo; Johanna Sandgren; Teresita Diaz de Ståhl; Philip Ewels; Valtteri Wirta; Monica Nistér; et al. (F1000Research, 2020)

Ten simple rules for making a software tool workflow-ready. - Paul Brack; Peter Crowther; Stian Soiland-Reyes; Stuart Owen; Douglas Lowe; Alan R. Williams; Quentin Groom; Mathias Dillen; Frederik Coppens; Björn A. Grüning; Ignacio Eguinoa; Philip Ewels; et al. (PLoS Comput. Biol., 2022)