niekwit/rna-seq-star-tetranscripts

Snakemake workflow for transposable element RNA-Seq using TEtranscripts

Overview

Latest release: v0.4.0, Last update: 2025-08-04

Linting: linting: failed, Formatting: formatting: failed

Topics: ngs-pipeline rna-seq-pipeline snakemake-workflow transposable-elements

Wrappers: bio/fastqc bio/samtools/index bio/samtools/view bio/trim_galore/pe

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/niekwit/rna-seq-star-tetranscripts . --tag v0.4.0

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.

config.yaml

Use config.yaml to set the parameters of the analysis.

The time setting in resources will only be relevant when running the pipeline on an HPC with the --slurm option.

samples.csv

Columns: sample: unique sample name (name of the reads file without .fastq.gz) genotype: genotype of the sample treatment: treatment condition of the sample reference: add yes if this sample should be set as a control in the differential transcript analysis batch: batch for each sample (e.g. different sequencing run). If more than one batch is present, a batch effect will be modelled during differential transcript analysis with DESeq2

Linting and formatting

Linting results

 1Workflow version: v0.4.0
 2Wrapper version: v5.5.1
 3ValueError in file "/tmp/tmp5s9wjm2e/niekwit-rna-seq-star-tetranscripts-1ab844e/workflow/scripts/general_functions.smk", line 23:
 4Following files not found:
 5reads/WT_1_R1_001.fastq.gz
 6reads/WT_1_R2_001.fastq.gz
 7reads/WT_2_R1_001.fastq.gz
 8reads/WT_2_R2_001.fastq.gz
 9reads/WT_3_R1_001.fastq.gz
10reads/WT_3_R2_001.fastq.gz
11reads/KO_1_R1_001.fastq.gz
12reads/KO_1_R2_001.fastq.gz
13reads/KO_2_R1_001.fastq.gz
14reads/KO_2_R2_001.fastq.gz
15reads/KO_3_R1_001.fastq.gz
16reads/KO_3_R2_001.fastq.gz
17  File "/tmp/tmp5s9wjm2e/niekwit-rna-seq-star-tetranscripts-1ab844e/workflow/Snakefile", line 26, in <module>
18  File "/tmp/tmp5s9wjm2e/niekwit-rna-seq-star-tetranscripts-1ab844e/workflow/scripts/general_functions.smk", line 23, in import_samples

Formatting results

 1[DEBUG] 
 2[WARNING] In file "/tmp/tmp5s9wjm2e/niekwit-rna-seq-star-tetranscripts-1ab844e/workflow/rules/mapping.smk":  Keyword "shell" at line 50 has comments under a value.
 3	PEP8 recommends block comments appear before what they describe
 4(see https://www.python.org/dev/peps/pep-0008/#id30)
 5[DEBUG] In file "/tmp/tmp5s9wjm2e/niekwit-rna-seq-star-tetranscripts-1ab844e/workflow/rules/mapping.smk":  Formatted content is different from original
 6[DEBUG] 
 7[DEBUG] In file "/tmp/tmp5s9wjm2e/niekwit-rna-seq-star-tetranscripts-1ab844e/workflow/rules/resources.smk":  Formatted content is different from original
 8[DEBUG] 
 9[DEBUG] In file "/tmp/tmp5s9wjm2e/niekwit-rna-seq-star-tetranscripts-1ab844e/workflow/rules/fastqc.smk":  Formatted content is different from original
10[DEBUG] 
11[DEBUG] In file "/tmp/tmp5s9wjm2e/niekwit-rna-seq-star-tetranscripts-1ab844e/workflow/rules/trimming.smk":  Formatted content is different from original
12[DEBUG] 
13[DEBUG] In file "/tmp/tmp5s9wjm2e/niekwit-rna-seq-star-tetranscripts-1ab844e/workflow/Snakefile":  Formatted content is different from original
14[DEBUG] 
15[DEBUG] In file "/tmp/tmp5s9wjm2e/niekwit-rna-seq-star-tetranscripts-1ab844e/workflow/rules/deseq2.smk":  Formatted content is different from original
16[DEBUG] 
17[DEBUG] 
18[DEBUG] In file "/tmp/tmp5s9wjm2e/niekwit-rna-seq-star-tetranscripts-1ab844e/workflow/rules/plotting.smk":  Formatted content is different from original
19[DEBUG] 
20[DEBUG] In file "/tmp/tmp5s9wjm2e/niekwit-rna-seq-star-tetranscripts-1ab844e/workflow/rules/te_quantification.smk":  Formatted content is different from original
21[INFO] 8 file(s) would be changed 😬
22[INFO] 1 file(s) would be left unchanged 🎉
23
24snakefmt version: 0.11.0