Rename_FASTQ

Quick Facts

Workflow Type	Applicable Kingdom	Last Known Changes	Command-line Compatibility	Workflow Level
Standalone	Any Taxa	PHB v2.1.0	Yes	Sample-level

Rename_FASTQ_PHB

This sample-level workflow receives a read file or a pair of read files (FASTQ), compressed or uncompressed, and returns a new, renamed and compressed FASTQ file.

Inputs

Terra Task Name	Variable	Type	Description	Default Value	Terra Status
rename_fastq_files	new_filename	String	New name for the FASTQ file(s)		Required
rename_fastq_files	read1	File	FASTQ file containing read1 sequences		Required
rename_fastq_files	read2	File	FASTQ file containing read2 sequences		Optional
rename_PE_files or rename_SE_files	cpu	Int	Number of CPUs to allocate to the task	2	Optional
rename_PE_files or rename_SE_files	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional
rename_PE_files or rename_SE_files	docker	String	The Docker container to use for the task	"us-docker.pkg.dev/general-theiagen/ubuntu/ubuntu:jammy-20230816"	Optional
rename_PE_files or rename_SE_files	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	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

If a reverse read (read2) is provided, the files get renamed to the provided new_filename input with the notation <new_filename>_R1.fastq.gz and <new_filename>_R2.fastq.gz. If only read1 is provided, the file is renamed to <new_filename>.fastq.gz.

Variable	Type	Description
read1_renamed	File	New read1 FASTQ file renamed to desired filename
read2_renamed	File	New read2 FASTQ file renamed to desired filename
rename_fastq_files_analysis_date	String	Date of analysis
rename_fastq_files_version	String	Version of PHB used for the analysis