Overview

The manual creation of Terra tables can be tedious and error-prone. This workflow will automatically create your Terra data table when provided with the location of the files.

Inputs

<aside> ⚠️ DEFAULT BEHAVIOR: Files with underscores and/or decimals in the sample name are not recognized; please use dashes instead. For example, name.banana.hello_yes_please.fastq.gz will become "name". This means that se-test_21.fastq.gz and se-test_22.fastq.gz will not be recognized as separate samples.

This can be changed by providing information in the file_ending optional input parameter. See below for more information

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Terra Inputs

Finding the `data_location_path`

Using the Terra data uploader
Using the “Files” section in the Data tab

How to determine the appropriate `file_ending` for your data

The file_ending should be a substring of your file names that is held in common. See the following examples:

One or more elements in common for all files:
No elements in common

To include multiple file endings, please separate them with commas, as shown in the “no elements in common” section.

Outputs

Your table will automatically appear in your workspace with the following fields:

Sample name (under the new_table_name_id column), which will be the section of the file’s name before any decimals or underscores (unless file_ending is provided)
- By default:
  - sample01.lane2_flowcell3.fastq.gz will be represented by sample01 in the table
  - sample02_negativecontrol.fastq.gz will be represented by sample02 in the table
- See “How to determine the appropriate file_ending for your data” above to learn how to change this default behavior
Your data in the appropriate columns, dependent on the values of assembly_data and paired_end

table columns assembly_data is true paired_end is true assembly_data AND paired_end are false

read1 ❌ ✅ ✅

read2 ❌ ✅ ❌

assembly_fasta ✅ ❌ ❌
The date of upload under the upload_date column
The name of the workflow under table_created_by, to indicate the table was made by the Create_Terra_Table_PHB workflow.

table columns	`assembly_data` is true	`paired_end` is true	`assembly_data` AND `paired_end` are false
read1	❌	✅	✅
read2	❌	✅	❌
assembly_fasta	✅	❌	❌

Workflows available