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» nextflow run nf-core/nascent -r 1.0 -profile test
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Introduction

This nascent transcription processing 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.

Reference

If you have used this pipeline in your research, please cite it using the DOI mentioned above.

Documentation

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

Arguments

Required Arguments

Argument Usage Description
-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

Arguments Usage Description
--outdir \</project/> Specifies where to save the output from the nextflow run.
--savefq Compresses and saves raw fastq reads.
--saveTrim Compresses and saves trimmed fastq reads.
--saveAll Compresses and saves all fastq reads.
--skipBAM Skips saving BAM files (only save CRAM). Default=False

Input File Options

Arguments Usage Description
--singleEnd Specifies that the input files are not paired reads (default is paired-end).
--flip Reverse complements each strand. Necessary for some library preps.

Performance Options

Arguments Usage Description
--threadfqdump Runs multi-threading for fastq-dump for sra processing.

QC Options

Arguments Usage Description
--skipMultiQC Skip running MultiQC.
--skipRSeQC Skip running RSeQC.

Credits

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.