Introduction

umcugenetics/dxnextflowrna is a bioinformatics pipeline that can be used to analyse human RNA sequencing data. It takes FASTQ files as input, performs quality control (QC), trimming, filtering and alignment, and produces an extensive QC report.

1. Read QC (FastQC)
2. Present QC for raw reads (MultiQC)
3. Adapter and quality trimming (Trim Galore!)
4. Removal of ribosomal RNA (SortMeRNA)
5. Alignment (STAR)
6. Merge, sort and index alignments (SAMtools)
7. UMI-based deduplication (UMI-tools)
8. Convert to CRAM (SAMtools)
9. Extensive quality control:
   1. RSeQC
   2. Preseq
10. Present QC (MultiQC)

Usage

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.

1. Create an input directory with sample's fastq files (paired, multiple lanes allowed.)
2. Clone the github repository and all dependencies if required.
3. Install

sh install.sh

4. Now, you can run the pipeline using:

<path_to_git_clone>/tools/nextflow/nextflow run \
<path_to_git_clone>/main.nf  \
-c <path_to_git_clone>/nextflow.config \
--input <input> \
--outdir <output> \
--analysis_id <analysis_id> \
--email <email> \
-resume \
-ansi-log false \
-profile singularity \

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.

For more details and further functionality, please refer to the usage documentation

Pipeline output

For more details about the output files and reports, please refer to the output documentation.

Developers: Instructions and reminders when changing DxNextflowRNA

Warning

Please, try to keep using nfcore tools and guidelines!

Update files

• Update all type of citations:
  • CITATIONS.md file.
  • toolCitationText and toolBibliographyText in utils_umcugenetics_dxnextflowrna_pipeline/main.nf
• Update version in nextflow.config and multiqc_config by using nf-core pipelines bump-version <new_version>
• Update metro map

When updating Nextflow

• Update version by using nf-core pipelines bump-version --nextflow <new_nextflow_version>
• Update version in install.sh and

  sh install.sh

Credits

umcugenetics/dxnextflowrna was originally written by UMCU Genetics.

Citations

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

You can cite the nf-core publication as follows:

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.