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.
pixelator amplicon
)pixelator preqc | pixelator adapterqc
)pixelator demux
)pixelator collapse
)pixelator graph
)pixelator annotate
)pixelator analysis
)pixelator layout
)pixelator report
)[!WARNING] Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity. This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable
NXF_APPTAINER_HOME_MOUNT
orNXF_SINGULARITY_HOME_MOUNT
totrue
in the machine from which you launch the pipeline.
[!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.
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/pixelator was originally written for Pixelgen Technologies AB by:
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).
If you use nf-core/pixelator for your analysis, please cite it using the following doi: 10.5281/zenodo.10015112
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.
You can cite the molecular pixelation technology as follows:
Molecular pixelation: spatial proteomics of single cells by sequencing.
Filip Karlsson, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, Sylvain Geny, Erik Pettersson, Jan Rhomberg-Kauert, Ludvig Larsson, Hanna van Ooijen, Stefan Petkov, Marcela González-Granillo, Jessica Bunz, Johan Dahlberg, Michele Simonetti, Prajakta Sathe, Petter Brodin, Alvaro Martinez Barrio & Simon Fredriksson
Nat Methods. 2024 May 08. doi: 10.1038/s41592-024-02268-9