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).