Concatenate Illumina Lanes¶

Quick Facts¶

Workflow Type	Applicable Kingdom	Last Known Changes	Command-line Compatibility	Workflow Level	Dockstore
Data Import, Standalone	Any taxa	v2.3.0	Yes	Sample-level	Concatenate_Illumina_Lanes_PHB

Concatenate_Illumina_Lanes_PHB¶

Some Illumina machines produce multi-lane FASTQ files for a single sample. This workflow concatenates the multiple lanes into a single FASTQ file per read type (forward or reverse).

Inputs¶

Terra Task Name	Variable	Type	Description	Default Value	Terra Status
concatenate_illumina_lanes	read1_lane1	File	The first lane for the forward reads		Required
concatenate_illumina_lanes	read1_lane2	File	The second lane for the forward reads		Required
concatenate_illumina_lanes	samplename	String	The name of the sample being analyzed		Required
cat_lanes	cpu	Int	Number of CPUs to allocate to the task	2	Optional
cat_lanes	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional
cat_lanes	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.2	Optional
cat_lanes	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional
concatenate_illumina_lanes	read1_lane3	File	The third lane for the forward reads		Optional
concatenate_illumina_lanes	read1_lane4	File	The fourth lane for the forward reads		Optional
concatenate_illumina_lanes	read2_lane1	File	The first lane for the reverse reads		Optional
concatenate_illumina_lanes	read2_lane2	File	The second lane for the reverse reads		Optional
concatenate_illumina_lanes	read2_lane3	File	The third lane for the reverse reads		Optional
concatenate_illumina_lanes	read2_lane4	File	The fourth lane for the reverse reads		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

Workflow Tasks¶

This workflow concatenates the Illumina lanes for forward and (if provided) reverse reads. The output files are named as followed:

Forward reads: <samplename>_merged_R1.fastq.gz
Reverse reads: <samplename>_merged_R2.fastq.gz

Outputs¶

Variable	Type	Description
concatenate_illumina_lanes_analysis_date	String	Date of analysis
concatenate_illumina_lanes_version	String	Version of PHB used for the analysis
read1_concatenated	File	Concatenated forward reads
read2_concatenated	File	Concatenated reverse reads