auto_process_ngs.commands.samplesheet_cmd
- auto_process_ngs.commands.samplesheet_cmd.edit_samplesheet(ap)
Bring up SampleSheet in an editor
- Parameters:
ap (AutoProcessor) – autoprocessor pointing to the analysis directory to operate on
- auto_process_ngs.commands.samplesheet_cmd.import_samplesheet(ap, new_sample_sheet)
Update the SampleSheet contents from a file
- Parameters:
ap (AutoProcessor) – autoprocessor pointing to the analysis directory to operate on
sample_sheet (str) – path or URL pointing to the SampleSheet file to import the contents from
- auto_process_ngs.commands.samplesheet_cmd.predict_samplesheet_outputs(ap)
Predict the outputs from the SampleSheet
- Parameters:
ap (AutoProcessor) – autoprocessor pointing to the analysis directory to operate on
- auto_process_ngs.commands.samplesheet_cmd.samplesheet(ap, cmd, *args, **kws)
Various sample sheet manipulations
- Parameters:
ap (AutoProcessor) – autoprocessor pointing to the analysis directory to operate on
cmd (int) – sample sheet operation to perform
args (list) – positional arguments specific to the command
kws (mapping) – keyword arguments specific to the command
- auto_process_ngs.commands.samplesheet_cmd.set_project(ap, new_project, lanes=None, where=None)
Update the project names in the SampleSheet
- Parameters:
ap (AutoProcessor) – autoprocessor pointing to the analysis directory to operate on
new_project (str) – new project name
lanes (list) – optional list of lane numbers to apply project name update to
where (tuple) – optional tuple ‘(COLUMN,PATTERN)’ to only apply update to lines where value in COLUMN matches glob-style PATTERN
- auto_process_ngs.commands.samplesheet_cmd.set_sample_id(ap, new_id, lanes=None, where=None)
Update the sample IDs in the SampleSheet
- Parameters:
ap (AutoProcessor) – autoprocessor pointing to the analysis directory to operate on
new_id (str) – new sample ID
lanes (list) – optional list of lane numbers to apply project name update to
where (tuple) – optional tuple ‘(COLUMN,PATTERN)’ to only apply update to lines where value in COLUMN matches glob-style PATTERN
- auto_process_ngs.commands.samplesheet_cmd.set_sample_name(ap, new_name, lanes=None, where=None)
Update the sample names in the SampleSheet
- Parameters:
ap (AutoProcessor) – autoprocessor pointing to the analysis directory to operate on
new_name (str) – new sample name
lanes (list) – optional list of lane numbers to apply project name update to
where (tuple) – optional tuple ‘(COLUMN,PATTERN)’ to only apply update to lines where value in COLUMN matches glob-style PATTERN
- auto_process_ngs.commands.samplesheet_cmd.view_samplesheet(ap)
Show the raw SampleSheet content
- Parameters:
ap (AutoProcessor) – autoprocessor pointing to the analysis directory to operate on