Flow Documentation

Partek Flow Documentation

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Click Import and the table will be created (Figure 5). Click Show data files to expand the table and associate files. For more details see the Adding samples section.

 

Numbered figure captions
SubtitleTextSample table created from a text file with attributes
AnchorNameSample table created from a text file with attributes

 

 

Include Data Import

 

If you have a text file that contains sample IDs and attributes as well as the filenames of your data, you can create the sample table and start the data import at the same time. This is particularly useful for projects where multiple files are associated with the same sample (e.g., a sample ran in multiple lanes in the sequencer).

For this type of import, the text file may be located in either the Partek Flow server, My computer, or from a URL.  HoweverHowever, the data files should already be uploaded to the Partek Flow server (see section on file transfers).
In the text file, each filename to be associated with the sample must be separated by a tab. That means, if you are using a spreadsheet software to generate the text file, there is a maximum of one file per column. You also need to add headers such as file1, file2, etc., to define the columns. There is no limit on the number of columns on the text file. It is possible to have a different number of files associated with different samples.

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Numbered figure captions
SubtitleTextText with attributes and filenames
AnchorNameText with attributes and filenames

 

Text file and data are in different directories

If text file containing the sample information and the data files to be imported are different directories, you must include the file paths. For text files located in the Partek Flow server, but in different directories, you can use relative or absolute file paths. For text files located in My Computer or URL (and the data is in the Partek Flow Server) you must use an absolute file path.

Relative

paths

path 

You can use a path relative to the location of the text file you are using to create the sample table. For example in Figure 7, the text file is located in a directory called "download" while the files are in a subdirectory called MyData, then the filenames must include the path /MyData/. An example would be: /MyData/NA1031_S25_L007_R1_001.fastq.gz

 

Numbered figure captions
SubtitleTextThe text file is located in a directory called "download" while the files are located in a directory one level below called "MyData"
AnchorNameThe text file is located in a directory called "download" while the files are located in a directory one level below called "MyData"

 

Absolute path

You can use the full path to the file based on your Partek Flow server.  You You must include the paths starting from the Partek Flow home directory (Figure 8, red box). For typical installations, the path begins with /home/flow/FlowData/ and so the filenames to include in the text file may look like this: /home/flow/FlowData/download/MyData/NA1031_S25_L007_R1_001.fastq.gz

 

Numbered figure captions
SubtitleTextThe Current directory (red box) shows the file path to be included in a text file containing absolute paths
AnchorNameThe Current directory (red box) shows the file path to be included in a text file containing absolute paths

 

Once you have selected the text file with filenames and/or file paths, click Next.  TThe text file will be summarized as in Figure 9. If the file types are valid, Partek Flow will recognize the filenames and locate the files within the directory.  The The Files column represent files to be imported.

 

Numbered figure captions
SubtitleTextSelecting the attributes, Sample ID and filenames
AnchorNameSelecting the attributes, Sample ID and filenames

 

 

Click Import and the table will be created. After a few seconds, the server icon Image Removed will will be animated (Figure 10). This means that the process of importing data files have started. Click the Queue dropdown and select View queued tasks... to see the queue of import tasks (Figure 11).

 

Numbered figure captions
SubtitleTextSample table created from a text file and data is queued for import
AnchorNameSample table created from a text file and data is queued for import

Numbered figure captions
SubtitleTextTask Queue showing import tasks for each sample
AnchorNameTask Queue showing import tasks for each sample


At this stage, you can also go to the Analyses Tab of the project and see that the data node has been created but the color is light blue, which indicates the import is not complete (Figure 12, left). Once all the files have been imported from the queue, the data node will appear darker (Figure 12, right).

 

Numbered figure captions
SubtitleTextAnalyses Tab showing data node during import (left) and once the import is completed (right)
AnchorNameAnalyses Tab showing data node during import (left) and once the import is completed (right)

 

To view the files associated with the data, go to the Data Tab and click Show data files to expand the table. Figure 13 shows that four files were successfully imported for each sample. You can add more or delete samples as described in the Adding samples section.

 

Numbered figure captions
SubtitleTextExpanded sample table created from a text file with attributes and associated data files
AnchorNameExpanded sample table created from a text file with attributes and associated data files

 

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