Automating Report Generation
Automated report generation is available via. the
do-ms_cmd.R script. To generate a report, simply run:
Rscript do-ms_cmd.R config_file.yaml
The configuration file is specified in the YAML file format. An annotated example can be found here
All files specified under
input_files must be specified in
global.R as part of the available input file list. If you’re using custom modules, or using a different search engine, please update the list in
For the fields
remove_contam, if you don’t wish to apply these filters, simply comment out the line in the config file by appending with the
Experiment short names specified in
exp_names are applied after filtering, i.e., to the list of raw files that survive the user-specified filters. If too few/too many names are listed, the program will assign them or ignore them accordingly. A map of short names to raw files can be outputted as a module.
Some, but not all, of the fields in the configuration file can also be specified via. the command line. This is useful for automated pipelines where programatically editing the config file would be problematic. View the available arguments by running
Rscript do-ms_cmd.R -h
Adding more options via. the command-line can be done by editing the beginning of the
do-ms_cmd.R script. Or, open a GitHub issue.