Rule sdge2sdgeAR:¶
Purpose¶
The dge2sdgeAR rule is designed to facilitate the utilization of the transcript-indexed spatial digital gene expression (SGE) matrix in NovaScope's reformatting features. The main function of Rule dge2sdgeAR is creating a link from the original SGE located at <output_directory>/align/<flowcell_id>/<chip_id>/<run_id>/sge to the directory <output_directory>/analysis/<run_id>/<unit_id>/sgeAR.
The use of the sgeAR subfolder instead of the direct sge directory allows for any necessary manual preprocessing of the SGE before reformatting. For more details, see The sgeAR Subfolder and Manual Preprocess.
Input Files¶
- Spatial Digital Gene Expression (SGE) Matrix and relevant files
Required input files include a SGE, its related visualizations, and the meta file for X Y coordinates, which are created by Rule
dge2sdge.
Output Files¶
The rule generates the following output in the specified directory path:
1 | |
These output files are identical to those produced by the dge2sdge rule, as dge2sdgeAR does not modify the files but merely relocates them for easier access and further processing.
Output Guidelines¶
No action is required.
Parameters¶
No additional parameter is applied in this rule.
Dependencies¶
Given the input from Rule dge2sdge serve as the input for sdge2sdgeAR, Rule sdge2sdgeAR can only execute if the input SGE is available or the dependent rules have successfully completed their operations. See an overview of the rule dependencies in the Workflow Structure.
Code Snippet¶
The code for this rule is provided in c01_sdge2sdgeAR.smk.