Introduction

This small demo test pipeline tries to replicate a simple MCMICRO run using core tools, only using nf-core modules.

Pipeline summary

To recreate a very basic pipeline similar to what MCMICRO does (without any bells and whistles), we first created a pipeline template using nf-core tools : nf-core create. Additional modules such as fastqc and multiqc were removed, as they are not used for imaging QC at this point. Several components of the nf-core template were removed if not needed, to make this demo as lightweight as possible, without confusing, non-used files. Modules that are already merged into nf-core/modules were installed

Pipeline setup

1. nf-core create
2. nf-core modules install coreograph
3. nf-core modules install cellpose
4. nf-core modules install deepcell/mesmer
5. nf-core modules install mcquant
6. nf-core modules install scimap/mcmicro

Credits

SchapiroLabor/mcmicro_nfcore_demo was originally written by SchapiroLabor.

We thank the following people for their contribution to nf-core modules used in this demo pipeline:

• Florian Wuennemann
• Adam Taylor
• Margot Chazotte
• Jose Nimo
• Chiara Schiller
• Kresimir Bestak
• Aroj Hada
• Miguel A. Ibarra-Arellano
• Victor Perez
• Wouter-Michiel Vierdag
• Luis Kuhn Cuellar
• Carolin Schwitalla
• Dominik Molitor
• Jelena Pejovic Simeunovic
• Svetozar Nesic
• Emilio Palumbo