Deconvolution of 10x Visium data using the tools below

• Cell2Location
• RCTD
• Stereoscope
• Seurat
• SPOTlight
• Tangram
• CARD
• STRIDE
• SpatialDWLS

Location on Minerva

/sc/arion/projects/HIMC/nextflow/visium_deconvolution

Example usage

nextflow run main.nf \
  --rna_h5ad /sc/arion/projects/HIMC/reference/single_cell_references/andrewLeader_plus_GSE131907_lung/andrewLeader_plus_GSE131907_lung.h5ad \ # Reference scanpy h5ad object
  --rna_h5Seurat /sc/arion/projects/HIMC/reference/single_cell_references/andrewLeader_plus_GSE131907_lung/andrewLeader_plus_GSE131907_lung.rds \ # Reference seurat or RDS object
  --outdir_final /sc/arion/projects/HIMC/himc-project-data/SAGN29/data/10X/SAGN29_40765_0_v5/deconvolution/andrewLeader_plus_GSE131907_lung/ \ # Save output location
  --spatial_h5ad /sc/arion/projects/HIMC/himc-project-data/SAGN29/data/10X/SAGN29_40765_0_v5 \ # Visium dataset
  --celltype_key Cell_type_final \ # Column in to use in Reference
  --c2l_batch Sample \ # Cell2Locaton Batch argument OPTIONAL
  --c2l_covariates Sample_Origin \ # Cell2Locaton Covariates argument OPTIONAL
  --c2l_cellsPerSpot 20 \ # Cell2Locaton Estimated Cells Per Spot argument OPTIONAL
  -w work/SAGN29_40765_0_v5 \
  -c nextflow.config

To run just one tool specify the argument below

  --tools RCTD

Or multiple tools (CAUTION can be buggy at times, would just run one tool instead of full user input

  --tools 'RCTD, Cell2Location'

Previous commands for huge batch (HCC, NSCLC, CRC etc.) can be found in

batch_cmds/

The scripts are grouped by organ. For example NSCLC

# sample list can be found in
Lung.samples

# script to run per sample
run_Lung.sh

# batch command can be found here
run_Lung.cmd

Notes

• If want want to test the tool in an interactive session instead of submitting a job, change the config parameter

-c nextflow_local.config

• You can use the GPU nodes to run Cell2location

-c nextflow_c2la100.config
--tools cell2location

• Docker images were either created by me or found on DockerHub. Image locations can be viewed in

-c nextflow.config

• Repo of Dockerfiles can be found here