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