nf-core

nf-core Intro

A community effort to collect a curated set of analysis pipelines built using Nextflow.

At UTD we have lots of core facilities. The genomics core, imaging core, etc…

and nf-core!

Testing a pipeline

Usually you’d need to refer to the nf-core installation docs.

However GitHub Codespaces cut out some of that work.

Let’s run:

nextflow run nf-core/rnaseq -profile test,docker --outdir results

Download the Multiqc Report

1. Open up the file explorer and navigate to results/multiqc/multiqc_report.html and right-click the html file and select Download.
2. Now that the MultiQC report is on your local computer open it up in a web browser. Preferably next to the pipeline’s output docs.

What’s MultiQC?

A tool that aggregate results from bioinformatics analyses across many samples into a single report.

MultiQC searches a given directory for analysis logs and compiles a HTML report. It’s a general use tool, perfect for summarizing the output from numerous bioinformatics tools.

Using nf-core pipelines in Snakemake

Snakemake 6.2 and later allows to hand over execution steps to other workflow management systems. By this, it is possible to make use of workflows written for other systems, while performing any further pre- or postprocessing within Snakemake.

Snakemake Docs

rule chipseq_pipeline:
    input:
        input="design.csv",
        fasta="data/genome.fasta",
        gtf="data/genome.gtf",
        # any --<argname> pipeline file arguments can be given here as <argname>=<path>
    output:
        "results/multiqc/broadPeak/multiqc_report.html",
    params:
        pipeline="nf-core/chipseq",
        revision="2.0.0",
        profile=["test", "docker"],
        # The chosen pipeline expects an --outdir to be given.
        # We infer this from the output file path. Since that file path can be changed
        # e.g. in case of cloud storage, we use a lambda function to infer the outdir.
        outdir=lambda wildcards, output: str(Path(output[0]).parents[-2]),
        # any --<argname> pipeline arguments can be given here as <argname>=<value>
    handover: True
    wrapper:
        "v3.12.1/utils/nextflow"

Snakemake Nextflow Wrapper Docs

Testing nf-core/rnaseq in Snakemake

Snakefile

rule rnaseq_pipeline:
    output:
        "results/multiqc/star_salmon/multiqc_report.html",
    params:
        pipeline="nf-core/rnaseq",
        revision="3.14.0",
        profile=["test", "docker"],
        outdir=lambda wildcards, output: str(Path(output[0]).parents[-2]),
    handover: True
    wrapper:
        "v3.12.1/utils/nextflow"

snakemake --cores 2

While you wait

You might compare the Snakemake rule and the nextflow run ... command that was used earlier to run the nf-core/rnaseq pipeline

Running the golden snidget Data

Snakefile

rule rnaseq_pipeline:
    input:
        "reads/BORED_1_R1.fq.gz",
        input="inputs/samplesheet.csv",
        fasta="refs/genome.fa",
        gff="refs/features.gff",
        transcript_fasta="refs/transcripts.fa",
    output:
        "results/multiqc/star_salmon/multiqc_report.html",
        # TODO Add count file
    params:
        pipeline="nf-core/rnaseq",
        revision="3.14.0",
        profile=["docker"],
        extra=["-c inputs/extra.config"],
        outdir=lambda wildcards, output: str(Path(output[0]).parents[-2]),
    handover: True
    wrapper:
        "v3.12.1/utils/nextflow"