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Concatenate Illumina Lanes

Quick Facts

Workflow Type Applicable Kingdom Last Known Changes Command-line Compatibility Workflow Level
Standalone Any Taxa PHB 2.3.0 Yes Sample-level

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, used to name the output files 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