Rename_FASTQ
Quick Facts
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.
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_PE_files
cpu Int
Number of CPUs to allocate to the task
2
Optional
rename_PE_files
disk_size Int
Amount of storage (in GB) to allocate to the task
100
Optional
rename_PE_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
memory Int
Amount of memory/RAM (in GB) to allocate to the task
2
Optional
rename_SE_files
cpu Int
Number of CPUs to allocate to the task
2
Optional
rename_SE_files
disk_size Int
Amount of storage (in GB) to allocate to the task
100
Optional
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_SE_files
memory Int
Amount of memory/RAM (in GB) to allocate to the task
2
Optional
rename_fastq_files
read2 File
FASTQ file containing read2 sequences
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