Concatenate_Column_Content

Quick Facts

Workflow Type	Applicable Kingdom	Last Known Changes	Command-line Compatibility	Workflow Level
Exporting Data From Terra	Any taxa	PHB v2.1.0	Yes	Set-level

Concatenate_Column_Content_PHB

This set-level workflow will create a file containing all of the items from a given column in a Terra Data Table. This is useful when you want to investigate a collection of result files. There is a video available with more information about the Concatenate_Column_Content workflow: 📺 Workflow Focus: Concatenate_Column_Content. Although this video refers to an older version of this workflow and various names may be changed, the concepts presented are still applicable.

Inputs

This workflow runs on the set level.

Include the extension

When you provide the name of the output file, be sure to include the extension. For example, if you want the output file to be a FASTA file, you should include the .fasta extension in the concatenated_file_name input variable. Otherwise, the workflow will create a file without any extension, which can cause problems when you try to open it with certain programs and operating systems.

Please note that this workflow cannot produce Excel files. If you need an Excel file, you can convert the output file to Excel using a program like Microsoft Excel or Google Sheets.

Terra Task Name	Variable	Type	Description	Default Value	Terra Status
concatenate_column_content	concatenated_file_name	String	The name of the output file. Include the extension, such as ".fasta" or ".txt".		Required
concatenate_column_content	files_to_cat	Array[File]	The column that has the files you want to concatenate.		Required
cat_files	cpu	Int	Number of CPUs to allocate to the task	2	Optional
cat_files	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional
cat_files	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1	Optional
cat_files	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional
cat_files	skip_extra_headers	Boolean	If the files you are concatenating have identical headers, you can include only the first instance of the header and skip all of the others so they do not appear duplicated in the concatenated file. To activate this, set to true.	false	Optional
version_capture	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0	Optional
version_capture	timezone	String	Set the time zone to get an accurate date of analysis (uses UTC by default)		Optional

Outputs

Prevent Output Overwriting

Please note that if you run this workflow on the same Terra set, the results will overwrite each other. We recommend either (1) renaming the output variable, or (2) creating a new set every time you run the workflow. Multiple sets containing the same samples can be created as long as the set names are unique.

Variable	Type	Description
concatenated_files	File	The file containing all of the items from the column you selected.
concatenate_column_content_version	String	The version of the repository the workflow is hosted in
concatenate_column_content_analysis_date	String	The date the workflow was run