Table 2 Configuration files and their usage

config.yml

Main configuration file required for running the pipeline. This file can be generated by running scAnalyzer with a directory provided.

1, Project-related information: project name, project title

2, QC: Percentage cutoff of mitochondria reads and user-defined gene groups, cell and gene filtering criteria

3, Run setting: SGE or Slurm, number of CPUs, harmonization methods, scaling factor

4, Path to sample metadata information, reference file for label transfer in Azimuth format [32], output directory, path to the DE comparison file

5, Settings for DE analysis

sys.yml

System configuration file under the pipeline source (src) directory. This file only needs to be set up once after pipeline installation.

1, Path to a directory to store h5ad files for cellxgene VIP loading

2, Path to all references for cell type label transfer

3, Detailed information about the reference datasets

4, Miscellaneous settings of the pipeline

config_DEG.yml

Configuration file for running the DE analysis separately. This file can be generated by running scDEG with a directory provided. Several items are the same as the config.yml file.

1, Path to a UMI count matrix in h5ad or RDS format

2, Path to a sample metadata information file

3, Run setting: SGE or Slurm

4, Path to the DE comparison file

5, Settings for DE analysis

config_ref.yml

Configuration file for building the reference for cell type label transfer. This file can be generated by running scRef with a directory provided.

1, Path to an h5ad file containing UMI count matrix and cell annotation

2, Detailed information about this reference, including which labels to be used for future label transfer

config_convert.yml

Configuration file for converting public data to the standardized format for cellxgene VIP and CellDepot loading. This file can be generated by running scRef with a directory provided.

1, Path to the data file in h5ad or RDS format

2, Miscellaneous setting on the outputs