racer-snake

Overview

Pipeline for analysis of bulk RNA-seq and ATAC-seq, analyzing reads (r) at accessible (a) chromatin (c) and expression (e) of RNA (r), using Snakemake as a workflow manager.

	RNA-seq	ATAC-seq
Purpose	Gene expression	Chromatin accessibility
Alignment	STAR in nf-core/rnaseq	bwa in nf-core/atacseq
Quantification	- Transcript quantification (RSEM) - Gene counting (RSEM)	Peak calling (MACS2)
Comparative analysis	Differential expression (DESeq2)	Differential accessibility (DiffBind)

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Modules

setup

The steup module reads from the input configuration file (config template: config/config.yaml) to:

1. make samplesheets (for nf-core --input)
2. make parameter files (for nf-core -params-file)
3. download reference genome files

The following rules are within the setup module:

• copy_inputs
• bulid_samplesheet
• write_rnaseq_nfc_params
• write_atacseq_nfc_params
• build_rnaseq_nfc_samplesheet
• build_atacseq_nfc_samplesheet
• download_reference

rnaseq

The rnaseq module analyzes RNA-seq data in the following steps:

1. run nf-core/rnaseq to produce gene counts
2. run DESeq2 to perform differential expression analysis
3. create an HTML and .docx report of DESeq2 results

The following rules are within the rnaseq module:

• nfcore_rnaseq
• deseq2_configs
• deseq2_samplesheet
• deseq2
• deseq2_report
• deseq2_tables

atacseq

The rnaseq module analyzes RNA-seq data in the following steps:

1. run nf-core/atacseq to produce gene counts
2. run (DiffBind) to perform differential accessibility analysis
3. create an HTML and .docx report of DiffBind results

The following rules are within the atacseq module:

• nfcore_atacseq
• diffbind_configs
• diffbind_samplesheet
• diffbind
• diffbind_report
• diffbind_tables

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Environment set up

The environment set up for racer-snake is a conda environment with Snakemake (v9.17.2) and Nextflow (v25.10.4) installed.

The racer-snake pipeline is configured to set up the conda environment in snakemake/workflow/envs/conda_setup.sh (which is souced when running the main controller script, racer-snake.sh).

In the conda set up file ([snakemake/workflow/envs/conda_setup.sh]), the versions of Snakemake and Nextflow can be changed if different versions of the software are desired.

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Pipeline execution

Example command

The pipeline can be run by invoking the main bash script, racer-snake.sh.

bash racer-snake.sh \
  --config config/config.yaml \
  --runtype dry-run \
  --executor slurm

Arguments

The main controller script is racer-snake.sh. The following argument options are:

Flag	Required?	Description	Options
--config, -c	✓	Path to config file	—
--runtype, -r	✓	How Snakemake is invoked	run dry-run
--executor, -e	✓	Executor/profile mode	slurm local

Detailed explanation of flags:

• --config, -c (required): Path to config file (see config/config.yaml for the required structure)

• --runtype, -r (required): How Snakemake is invoked

  • runtype — executes normally
  • dry-run — passes --dry-run flag to Snakemake

• --executor, -e (required): Executor mode / profile selection

  • slurm — enables slurm executor with slurm directives
  • local — runs pipeline on the local machine

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Development

The racer-snake pipeline is still being developed.

Software versions used for develpment and testing

Base software

• Snakemake v9.17.2
• Nextflow v25.10.4
• R v4.5.3
  • Bioconductor v3.23
  • see renv.lock for all versions of R packages

RNA-seq tools

• nf-core/rnaseq v3.23.0-g13328f7
  • Base config for nextflow in nf-core/rnaseq: rnaseq/conf/base.config
• DESeq2 v1.52.0

ATAC-seq tools

• nf-core/rnaseq v2.1.2
  • Base config for Nextflow in nf-core/atacseq: atacseq/conf/base.config
• DiffBind v3.20.0