nf-core/molkart is a pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH). It takes as input a table of FISH spot positions (x,y,z,gene), a corresponding DAPI image (tiff format) and optionally a membrane staining image in tiff format. nf-core/molkart performs end-to-end processing of the data including image processing, QC filtering of spots, cell segmentation, spot to cell assignment and reports quality metrics such as the spot assignment rate, average spots per cell and segmentation mask size ranges.

  1. Read QC (FastQC)
  2. Present QC for raw reads (MultiQC)



If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Now, you can run the pipeline using:

nextflow run nf-core/molkart \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>
nextflow run nf-core/molkart \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.


nf-core/molkart was originally written by @FloWuenne.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don’t hesitate to get in touch on the Slack #molkart channel (you can join with this invite).


An extensive list of references for the tools used by the pipeline can be found in the file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.