The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.


If you’ve used this pipeline in your research, you can cite this pipeline using DOI 10.17605/OSF.IO/SV4UB (OSF project).


The nf-core/nascent pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting

This pipeline is designed to process the sequencing output of nascent transcription assays, like GRO-seq or PRO-seq. It produces bedGraph- and bigWig-fomatted outputs after mapping strand-specific reads, as well as other useful outputs like quality control reports or IGV-ready (Integrative Genomics Viewer) tdf files.

Quick start

Edit the appropriate config file, e.g. conf/slurm_grch38.config, to ensure the proper paths are set for genome reference files and other executables (look for all mentions of COMPLETE_*). Variable names should hopefully be self-explanatory. You can specify the Nextflow working directory and output directory with flags. Note you must also now specify the email to which the report will be sent for the run.

nextflow run nf-core/nascent --reads '*_R{1,2}.fastq.gz' -profile standard,docker


Required Arguments

-profile<base,slurm>Configuration profile to use.
—fastqs</project/*_{R1,R2}*.fastq>Directory pattern for fastq files.
—sras</project/*.sra>Directory pattern for sra files.
—genome_id<‘hg38’>Genome ID to which the samples will be mapped (e.g. hg38, mm10, rn6).
—workdir</project/tmp/>Nextflow working directory where all intermediate files are saved.
—email<EMAIL>Where to send workflow report email.

Save Options

—outdir</project/>Specifies where to save the output from the nextflow run.
—savefqCompresses and saves raw fastq reads.
—saveTrimCompresses and saves trimmed fastq reads.
—saveAllCompresses and saves all fastq reads.
—skipBAMSkips saving BAM files (only save CRAM). Default=False

Input File Options

—singleEndSpecifies that the input files are not paired reads (default is paired-end).
—flipReverse complements each strand. Necessary for some library preps.

Performance Options

—threadfqdumpRuns multi-threading for fastq-dump for sra processing.

QC Options

—skipMultiQCSkip running MultiQC.
—skipRSeQCSkip running RSeQC.


nf-core/nascent was originally written by Ignacio Tripodi (@ignaciot) and Margaret Gruca (@magruca).

Many thanks to the nf-core team and all who provided invaluable feedback and assistance along the way, particularly to @apeltzer, @ewels, @drpatelh, and @pditommaso.