To group jobs in the NextGENe AutoRun tool
You can load multiple samples for analysis with the same job options. You can then use the Group Jobs option to automatically group the samples into separate jobs. The same job options are applied to all the separate jobs.
1. If you have not already done so, on the Job File Editor window main menu, click Edit > Group Samples into Jobs.
The Group Jobs dialog box opens. The dialog box displays all the sample files that are currently loaded in the NextGENe AutoRun tool.
2. Specify how to group the samples.
Setting | Description |
|---|---|
Group by Sections | Group the jobs based on a user-defined section in the sample file names. The default values for delimiters are a dash (-), a period (.), and an underscore (_). For example, a sample file named F_R1_converted.fasta would have four sections based on the default underscore and period delimiters: • Section 1 = F • Section 2 = R1 • Section 3 = converted • Section 4 = fasta |
Group by Fixed Position | Group by user-specified position or range of positions in the sample file names. |
Group by Order | Group the jobs based on the order in which the sample files were loaded in to the NextGENe AutoRun tool AutoRun tool. |
 | The last grouping option that was selected remains selected by default when the Group Jobs dialog box opens. |
3. By default, the Job ID for each group is automatically created based on how the jobs are grouped. You do have the option of modifying some of the settings that affect how the Job ID is created.
Job Grouping | Default Group Name |
|---|---|
By Sections | The Group ID: section(s) indicates which section of the file name is used to group the sample files. This section is also used for the Job ID. For example, for the following six sample files with the Group ID: section(s) = 1 for grouping: • F_R1_converted.fasta • D_R1_converted.fasta • E_R1_converted.fasta • F_R2_converted.fasta • D_R2_converted.fasta • E_R2_converted.fasta creates three jobs with two sample files each and each job identified by one of the following three JOB IDs: F, D, or E. |
By Fixed Position | The Job ID is based on the user-specified character (for example, 1) or range of characters (for example, 1-4) in the file names that were used to group the jobs. For example, considering the same sample files above, using Group ID: character(s) = 1 for grouping creates three jobs with two sample files each and each job identified by one of the following three Job IDs: F, D, or E. Note: You can select Match Case to further refine the grouping and the Job IDs. |
By Order | By default, Group ID: the first item name is selected, which means that the ID that is assigned to each job is based on the name of the first file in each group. For example, considering the same sample files above, and using a Group Size = 2, then three jobs would be created with two sample files per group and each job identified by one of the following three Job IDs: • F_R1_converted • D_R1_converted • E_R1_converted Note: If you clear <Group ID: the first item name>, then the Job ID is a numeric value and it is created based on the order in which they groups are listed in the Group Jobs dialog box (e.g., 1, 2, 3, and so on). |
4. Optionally, build out the Job ID by assigning a prefix and/or suffix to the Group ID. For example:
• If the Group ID for three separate jobs is “D,” “E,” and “F,” then specifying Sample in the first blank Build Job Name field results in Job IDs of “SampleD,” “SampleE,” and “SampleF.”
• If you specified another value in the second blank Build Job Name field (such as the date of the job), then the job IDs would be “SampleD08062014,” “SampleE08062014,” and “SampleF08062014.”
5. Return to Step 5 or Step 15 as appropriate in To create a new job file in the NextGENe AutoRun tool.