Configuration

You need one configuration file and one annotation file to run the complete workflow. If in doubt read the comments in the config and/or try the default values.

• project configuration (config/config.yaml): different for every project/dataset and configures the analyses to be performed.
• sample annotation (sample_annotation): CSV file consisting of two mandatory columns
  • bam: absolute path to mapped/aligned (and filtered) BAM file (*.bam).
  • group:
    • bulk samples: a string describing a group of samples to be merged (e.g., RNA_untreated), which are visualized together as one genome track. Note: multiple rows can have the same group and the respective BAM files will be merged using samtools.
    • single-cell samples: path to a tab-separated metadata table wihtout header (TSV) where the first column are cell barcodes (CB) and the second a group variable (e.g., untreated/treated or cluster_1). Note: each single-cell BAM file is split into multiple BAM files according to the metadata file using sinto, and subsequenytly merged by group across all samples using samtools and downstream processed and visualized the same as bulk samples. It is important that the single-cell metadata.tsv is sample specific, because simply by chance different samples could have the same cell barcodes (CB).

Set workflow-specific resources or command line arguments (CLI) in the workflow profile workflow/profiles/default.config.yaml, which supersedes global Snakemake profiles.