Sequencing QC Pipeline

A Nextflow pipeline to perform quality control of sequencing data.

The pipeline was created to run on the ETH Euler cluster and it relies on the server's Lmod environment modules. Thus, the pipeline needs to be adapted before running it in a different HPC cluster.

Pipeline steps

1. FastQC
2. FastQ Screen
3. Trim Galore
4. FastQC
5. MultiQC

Required parameters

Path to the folder where the FASTQ files are located. --input

--input /cluster/work/nme/data/josousa/project/fastq/*fastq.gz

Output directory where the files will be saved. --outdir

--outdir /cluster/work/nme/data/josousa/project

Input optional parameters

• Option to force the pipeline to assign input as single-end. --single_end

  By default, the pipeline detects whether the input files are single-end or paired-end.

FastQ Screen optional parameters

• Option to provide a custom FastQ Screen config file.

  # Default
  --fastq_screen_conf '/cluster/work/nme/software/config/fastq_screen.conf'

• Option to pass the flag --bisulfite to FastQ Screen. --bisulfite

Sequencing method optional parameters

• Option to choose the sequencing method. This will adapt the default parameters to the method.

  # PBAT
  --seq_method 'PBAT'
  
  # RRBS
  --seq_method 'RRBS'
  
  # Single-cell
  --seq_method 'Single-cell'

  The default parameters for each sequencing method.

  # PBAT 
  fastq_screen_args='--bisulfite'
  trim_galore_args='--clip_R1 9 --clip_R2 9'
  
  # RRBS
  fastq_screen_args='--bisulfite'
  trim_galore_args='--rrbs'
  
  # Single-cell
  trim_galore_args='--clip_R1 6 --clip_R2 6'

Skipping options

• Option to skip FastQ Screen. --skip_fastq_screen

• Option to skip Trim Galore. --skip_trim_galore

Extra arguments

• Option to add extra arguments to FastQC. --fastqc_args

• Option to add extra arguments to FastQ Screen. --fastq_screen_args

• Option to add extra arguments to Trim Galore. --trim_galore_args

• Option to add extra arguments to MultiQC. --multiqc_args

Acknowledgements

This pipeline was adapted from the Nextflow pipelines created by the Babraham Institute Bioinformatics Group and from the nf-core pipelines. We thank all the contributors for both projects. We also thank the Nextflow community and the nf-core community for all the help and support.