tucca-cellag/tucca-rna-seq

[UNDER-CONSTRUCTION] TUCCA’s RNA-Seq Snakemake Workflow for Cellular Agriculture Projects

Overview

Topics:

Latest release: None, Last update: 2025-03-03

Linting: linting: failed, Formatting:formatting: passed

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it is recommended to install Miniforge. More details regarding Mamba can be found here.

When using Mamba, run

mamba create -c conda-forge -c bioconda --name snakemake snakemake snakedeploy

to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via

conda activate snakemake

Step 2: Deploy workflow

With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:

mkdir -p path/to/project-workdir
cd path/to/project-workdir

In all following steps, we will assume that you are inside of that directory. Then run

snakedeploy deploy-workflow https://github.com/tucca-cellag/tucca-rna-seq . --tag None

Snakedeploy will create two folders, workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.

Step 3: Configure workflow

To configure the workflow, adapt config/config.yml to your needs following the instructions below.

Step 4: Run workflow

The deployment method is controlled using the --software-deployment-method (short --sdm) argument.

To run the workflow with automatic deployment of all required software via conda/mamba, use

snakemake --cores all --sdm conda

Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment in step 2.

For further options such as cluster and cloud execution, see the docs.

Step 5: Generate report

After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using

snakemake --report report.zip

Configuration

The following section is imported from the workflow’s config/README.md.

General settings

To configure this workflow, modify config/config.yaml according to your needs, following the explanations provided in the file.

`DESeq2` differential expression analysis

To run the differential expression analysis, you must tell DESeq2 which sample annotations to use (annotations are columns in the samples.tsv file described below). This is done in the config.yaml file with the entries under diffexp:.

Sample and Unit Sheets

The sample and unit sheet setup is specified via tab-separated tabular files (.tsv). Each sample refers to an actual physical sample, and replicates (both biological and technical) may be specified as separate samples. Each sample, may correspond to one or more sequencing units (for example if you have several runs or lanes per sample).

Missing values can be specified by empty columns or by writing NA.

Sample Sheet (`samples.tsv`)

For each sample, add a line to the sample sheet in config/samples.tsv. For each sample, you will always have to specify a sample_name.

In addition, all variables_of_interest and batch_effects specified in the config/config.yaml under the diffexp: entry, will have to have corresponding columns in the config/samples.tsv.

Finally, the sample sheet can contain any number of additional columns, so if you are in doubt about whether you might at some point need some metadata you already have at hand, just add it to the sample sheet. Your future self will thank you.

`samples.tsv` Example

sample_name	treatment_1	treatment_2	sequencing_batch
A	untreated	untreated	1
B	untreated	treated	1
C	treated	untreated	1
D	treated	untreated	2
E	treated	treated	2

Unit Sheet (`units.tsv`)

For each sample, add one or more sequencing unit lines (runs, lanes or replicates) to the unit sheet in config/units.tsv.

`.fastq` file source

For each unit, you will have to define a source for your .fastq files. This can be done via the columns fq1, fq2 and sra, with either of:

A single .fastq file for single-end reads (fq1 column only; fq2 and sra columns present, but empty). The entry can be any path on your system, but we suggest something like a raw/ data directory within your analysis directory.
Two .fastq files for paired-end reads (columns fq1 and fq2; column sra present, but empty). As for the fq1 column, the fq2 column can also point to anywhere on your system.
[NOT IMPLEMENTED YET] A sequence read archive (SRA) accession number (sra column only; fq1 and fq2 columns present, but empty). The workflow will automatically download the corresponding .fastq data (currently assumed to be paired-end). The accession numbers usually start with SRR or ERR and you can find accession numbers for studies of interest with the SRA Run Selector. If both local files and an SRA accession are specified for the same unit, the local files will be used.

`units.tsv` Example

sample_name	unit_name	fq1	fq2
A	lane1	A.1.fq.gz	A.2.fq.gz
A	lane2	A2.1.fq.gz	A2.2.fq.gz
B	lane1	B.1.fq.gz	B.2.fq.gz
C	lane1	C.1.fq.gz	C.2.fq.gz
D	lane1	D.1.fq.gz	D.2.fq.gz
E	lane1	E.1.fq.gz	E.2.fq.gz

config.yaml

This file contains the general workflow configuration. Configurable options should be explained in the comments above the respective entry or right here in this config/README.md section.

Linting and formatting

Linting results

WorkflowError in file /tmp/tmpgu7ejeyh/workflow/Snakefile, line 6:
Expecting Snakemake version 8.27.1 or higher (you are currently using 8.25.5).

Formatting results

None