sc_config.yaml

#--- organism annotation

organism_defaults: ### FILL HERE ###  (e.g. Homo_sapiens.yaml)

organism:
  __options__: [name, genus, taxon, files, star_index, salmon_index, R]
  ### OVERWRITE ###  organism defaults (e.g. gtf, genome and indices)
  files:
    cellranger_transcriptome: ""   ### FILL HERE ###  (the transcriptome to use with CellRanger)
    cellranger_gtf: ""   ### FILL HERE ###  (the gtf to use with CellRanger)


#--- general pipeline parameters

pipeline_param:
  __options__: [out_path_pattern, log_path_pattern, in_path_pattern, feature_ref]
  
  in_path_pattern: ### FILL HERE ###  (path pattern where fastq files are stored)

  feature_ref: ""  ### FILL HERE ###  (if feature barcoding was used)


#--- parameters for rules

rule_options:
  __options__: [cellranger_count, velocyto_run]


#--- parameters for the jupyter notebook
jupyter_notebook:
  __options__: [snippet_parameters, defaults, report_snippets]