bakerwm/snakemake-rnaseq-star

Snakemake workflow for RNAseq using STAR and DESeq2

Overview

Topics:

Latest release: None, Last update: 2023-12-26

Linting: linting: failed, Formatting:formatting: failed

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/bakerwm/snakemake-rnaseq-star . --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 configuration

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

`DESeq2` differential expression analysis configuration

To successfully run the differential expression analysis, you will need to 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:. The comments for the entries should give all the necessary infos and linkouts. But if in doubt, please also consult the DESeq2 manual.

Sample and unit setup

The sample and unit setup is specified via tab-separated tabular files (.tsv). Missing values can be specified by empty columns or by writing NA.

sample sheet

The default sample sheet is config/samples.tsv (as configured in config/config.yaml). Each sample refers to an actual physical sample, and replicates (both biological and technical) may be specified as separate samples. 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 in doubt about whether you might at some point need some metadata you already have at hand, just put it into the sample sheet already---your future self will thank you.

unit sheet

The default unit sheet is config/units.tsv (as configured in config/config.yaml). For each sample, add one or more sequencing units (for example if you have several runs or lanes per sample).

`.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.
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.

adapter trimming

If you set trimming: activate: in the config/config.yaml to True, you will have to provide at least one cutadapt adapter argument for each unit in the adapters column of the units.tsv file. You will need to find out the adapters used in the sequencing protocol that generated a unit: from your sequencing provider, or for published data from the study's metadata (or its authors). Then, enter the adapter sequences into the adapters column of that unit, preceded by the correct cutadapt adapter argument.

strandedness of library preparation protocol

To get the correct geneCounts from STAR output, you can provide information on the strandedness of the library preparation protocol used for a unit. STAR can produce counts for unstranded (none - this is the default), forward oriented (yes) and reverse oriented (reverse) protocols.
Enter the respective value into a strandedness column in the units.tsv file.

Linting and formatting

Linting results

/tmp/tmpr1pxvt92/workflow/scripts/utils.py:175: SyntaxWarning: invalid escape sequence '\*'
  """
/tmp/tmpr1pxvt92/workflow/scripts/utils.py:227: SyntaxWarning: invalid escape sequence '\.'
  p = re.compile(f"\.f(ast)?({ext})(\.gz)?$", flags=re.IGNORECASE)
/tmp/tmpr1pxvt92/workflow/scripts/utils.py:227: SyntaxWarning: invalid escape sequence '\.'
  p = re.compile(f"\.f(ast)?({ext})(\.gz)?$", flags=re.IGNORECASE)
Traceback (most recent call last):
  File "/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py", line 1884, in args_to_api
    any_lint = workflow_api.lint()
               ^^^^^^^^^^^^^^^^^^^
  File "/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py", line 344, in lint
    workflow.include(
  File "/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py", line 1363, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/tmp/tmpr1pxvt92/workflow/Snakefile", line 27, in <module>
    # ##### target rules #####
  File "/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py", line 1363, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/tmp/tmpr1pxvt92/workflow/rules/common.smk", line 7, in <module>
    ftp = FTP.RemoteProvider()

... (truncated)

Formatting results

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[DEBUG] In file "/tmp/tmpr1pxvt92/workflow/rules/ref.smk":  Formatted content is different from original
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[DEBUG] In file "/tmp/tmpr1pxvt92/workflow/rules/design.smk":  Formatted content is different from original
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[DEBUG] In file "/tmp/tmpr1pxvt92/workflow/Snakefile":  Formatted content is different from original
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[DEBUG] In file "/tmp/tmpr1pxvt92/workflow/rules/common.smk":  Formatted content is different from original
[INFO] 4 file(s) would be changed 😬
[INFO] 7 file(s) would be left unchanged 🎉

snakefmt version: 0.8.5