output.md

merge_fastq: Output

This document describes the output produced by the pipeline.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

• merge_fastq - Merge FastQ files

merge_fastq

This script is based on the merge_and_rename_NGI_fastq_files.py standalone script from SciLifeLab. FastQ files are expected to have the typical Illumina naming convention (Ex: SampleName_S1_L001_R1_001.fastq.gz) to make sure that lanes are merged correctly.

Example: fastq_files/E3387-1t_S9_L001_R1_001.fastq.gz fastq_files/E3387-1t_S9_L002_R1_001.fastq.gz are merged as E3387-1t_R1.fastq.gz

fastq_files/E3387-3t_S10_L001_R1_001.fastq.gz
fastq_files/E3387-3t_S10_L003_R1_001.fastq.gz
fastq_files/E3387-3t_S11_L001_R1_001.fastq.gz
fastq_files/E3387-3t_S11_L002_R1_001.fastq.gz
	are merged as ./E3387-3t_R1.fastq.gz

Output directory: merged_fastq_files/

• merge_log
  • Text report showing which original FastQ files were merged together
• *fastq.gz
  • FastQ files after merging lanes for each sample