nf-core/pixelator

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Introduction

*nf-core/pixelator* is a bioinformatics best-practice analysis pipeline for analysis of Molecular Pixelation assays.
It takes a samplesheet as input and will process your data using pixelator to produce final antibody counts.

1. Build amplicon from input reads (pixelator amplicon)
2. Read QC and filtering, correctness of the pixel binding sequence sequences (pixelator preqc | pixelator adapterqc)
3. Assign a marker (barcode) to each read (pixelator demux)
4. Error correction, duplicate removal, compute read counts (pixelator collapse)
5. Compute the components of the graph from the edge list in order to create putative cells (pixelator graph)
6. Call and annotate cells (pixelator annotate)
7. Analyze the cells for polarization and colocalization (pixelator analysis)
8. Report generation (pixelator report)

Usage

:::note
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.
:::

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,design,panel,fastq_1,fastq_2  
uropod_control,D21,human-sc-immunology-spatial-proteomics,uropod_control_300k_S1_R1_001.fastq.gz,uropod_control_300k_S1_R2_001.fastq.gz  

Each row represents a sample and gives the design, a panel file and the input fastq files.

Now, you can run the pipeline using:

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

:::warning
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.

Credits

nf-core/pixelator was originally written for Pixelgen Technologies AB by:

• Florian De Temmerman
• Johan Dahlberg
• Alvaro Martinez Barrio

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 #pixelator channel (you can join with this invite).

Citations

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