Xenium Lung NE Plasticity

This repository contains the nextflow pipeline and scripts to analyze Xenium data for lung NE plasticity project.

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, where each row contains the sample name, path to Xenium Ranger output.

samplesheet.csv:

sample, xenium
CONTROL_REP1, xenium_output_folder

Next, prepare a parameter YAML file that looks as follows:

params.yml:

samplesheet: "../results/samplesheet.csv"             # path to the sample sheet
outdir: "../results/"                                 # output folder
experiment:
  name: "Xenium"
QC:
  gene_information_file: "../data/annotation.csv"     # gene annotation file
  extra_markers: "PHOX2B"                             # custom markers to plot
max_memory: "36.GB"                                   # memory
max_cpus: 6                                           # cpu

Now, you can run the pipeline. For local run on HPC with singularity installed, execute the following command

nextflow run ./main.nf \
   -profile singularity \
   -params-file ./params.yml \
   -w ./work/

If you are using MSKCC lilac, you can use the pre-defined lilac profile that uses the LSF executor.

nextflow run ./main.nf \
   -profile lilac \
   -params-file ./params.yml \
   -w ./work/