Introduction

gallvp/prepngs is a bioinformatics pipeline that pre-processes NGS data for downstream reuse across various pipelines.

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flowchart LR
  samplesheet(samplesheet.csv) ==> BAM2FASTQ
  samplesheet ==> FASTQC

  BAM2FASTQ ==> FASTQC
  FASTQC ==> FASTP
  FASTP ==> FASTQC2[FASTQC]

  FASTP ==> CAT
  CAT ==> FQ2FA

  CAT ==> fqout(FastQ)
  FQ2FA ==> faout(Fasta)

  FASTQC2 ==> multiqcout(MultiQC)

  subgraph Outputs[" "]
  multiqcout
  fqout
  faout
  end

  classDef bk fill:#0000
  class Outputs bk

Loading

1. BAM to FastQ (PBTK, optional)
2. Raw read QC (FastQC)
3. Adapter trimming (FASTP)
4. Trimmed read QC (FastQC)
5. Cat trimmed reads by group (cat, optional)
6. Convert trimmed reads to Fasta (Seqkit, optional)
7. Present QC (MultiQC)

Usage

Refer to usage, parameters and output documents for details.

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,group,reads_1,reads_2
test1,,r1.fastq.gz,r2.fastq.gz
test2,group1,sampleA.ccs.bam
test3,group1,sampleC.ccs.bam

Each row represents a sample with a single fastq/bam file (single-end) or a pair of fastq files (paired end). group column is optional. When present, it is used to concatenate the samples.

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Now, you can run the pipeline using:

nextflow run gallvp/prepngs \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Plant&Food Users

Download the pipeline to your /workspace/$USER folder. Change the parameters defined in the pfr/params.json file. Submit the pipeline to SLURM for execution.

sbatch ./pfr_prepngs

Credits

gallvp/prepngs was originally written by Usman Rashid.

The pipeline uses nf-core modules contributed by following authors:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.