This document describes the output produced by the pipeline.
The pipeline is built using Nextflow and processes data using the following steps:
- merge_fastq - Merge FastQ files
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