Sample sheet manipulation using `auto_process samplesheet`

The samplesheet command provides functionality for interrogating and manipulating the Illumina sample sheet control file.

Default sample sheet

The default sample sheet file is set in the parameters of the current analysis directory; all operations will be performed using this sample sheet.

When the samplesheet command is invoked without arguments then the path and contents of the default sample sheet are displayed.

The default sample sheet file can be updated with the --use option, for example:

auto_process.py samplesheet --use new_samplesheet.csv

Predicting outputs

The -p/--predict argument shows the predicted outputs from the sample sheet.

Updating project and sample names in batch

The following arguments enable key data in the sample sheet to be updated in batch:

--set-project: set the sample project for some or all lines in the file;
--set-sample-id: set the sample ID for some or all lines in the file (typically to synchronise the IDs with the sample names);
--set-sample-name: set the sample project for some or all lines in the file (typically to synchronise the names with the sample IDs).

The same syntax is used for the --set-* functions to specify the new values and to optionally select subsets of lines to apply the updates to:

[LANES:][COL=PATTERN:]NEW_VALUE

where LANES specifies one or more lane numbers (for example: 1, 1,2,3, 1-3, 1,3-5 etc), and COL specifies the name of a column in the sample sheet where lines will be selected only if the value in that column matches the glob-style PATTERN (for example: Sample_Name=ITS*).

Manually editing the sample sheet

The -e/--edit argument brings up the sample sheet in an editor to allow changes to be made manually.

Importing a new sample sheet file

The -i/--import argument enables content from a new file to be imported into the analysis directory and used as the new default sample sheet.

The imported file can be a local or remote file, or a URL, for example:

auto_process.py samplesheet -i user@remote.com:/Data/new_samplesheet.csv

Note

Importing differs from the --use argument in that a copy of the imported file is made within the analysis directory (whereas --use simply changes the location that the default sample sheet parameter points to).

Sample sheet manipulation using auto_process samplesheet