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Analysis Workflows for our study : SuperCell2.0 enables semi-supervised construction of multimodal metacell atlases

  • Benchmark Supercell2.0 against SEACells and metacell-2 on single-cell multimodal data.
  • Analyse intermodality consistency at the metacell level.
  • Benchmark the construction of the PBMC CITE-seq metacell atlas with semi-supervised and unsupervised workflows using our metacell tool SuperCell2.0 and STACAS.
  • Annotate and analyze the semi-supervised PBMC CITE-seq metacell atlas.

Additional data

Additional data (eg. containers, transcription factor motifs pfm matrix, gene signatures from the literature) required for this workflow are availbale on zenodo

Launch the snakemake workflow (snakemake v7.15.2) on a cluster with slurm and singularity

Workflow env

This workflow has been developped using snakemake v7.15.2. You can install our workflow conda env like this:

conda env create -n snakemake -f config/snakemake_v7.15.2.yml

load singularity module

module load singularityce

launch snakemake

conda activate snakemake

snakemake -j 30 \
    -kps snakefile_manuscript.py \
    --configfile config/workflow.yml \
    --use-singularity \
    --conda-frontend conda \
    --cluster-config config/cluster.yml \
    --cluster "sbatch -A {cluster.account} \
    -p {cluster.partition} \
    -N {cluster.N} \
    -t {cluster.time} \
    --job-name {cluster.name} \
    --mem {cluster.mem} \
    --cpus-per-task {cluster.cpus-per-task}\
    --output {cluster.output} \
    --error {cluster.error}"