niekwit/chip-seq
Snakemake workflow for ChIP-Seq analysis
Overview
Latest release: v0.5.0, Last update: 2026-04-09
Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=niekwit/chip-seq
Quality control: linting: failed formatting: failed
Deployment
Step 1: Install Snakemake and Snakedeploy
Snakemake and Snakedeploy are best installed via the Conda package manager. It is recommended to install conda via Miniforge. Run
conda create -c conda-forge -c bioconda -c nodefaults --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
For other installation methods, refer to the Snakemake and Snakedeploy documentation.
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/chip-seq . --tag v0.5.0
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.
Describe how to configure the workflow (using config.yaml and maybe additional files). All of them need to be present with example entries inside of the config folder.
Workflow parameters
The following table is automatically parsed from the workflow’s config.schema.y(a)ml file.
Parameter |
Type |
Description |
Required |
Default |
|---|---|---|---|---|
genome |
string |
Ensembl genome |
yes |
|
ensembl_genome_build |
integer |
Ensembl genome build |
yes |
|
deeptools |
yes |
|||
. bigwig |
||||
. . binSize |
integer |
|||
. . normalizeUsing |
string |
|||
. . extra |
string |
|||
. computeMatrix |
||||
. . mode |
string |
|||
. . referencePoint |
string |
|||
. . regionBodyLength |
integer |
|||
. . upstream |
integer |
|||
. . downstream |
integer |
|||
. . binSize |
integer |
|||
. . averageTypeBins |
string |
|||
. . regionsFileName |
string |
|||
. . no_whole_genome |
boolean |
|||
. . extra |
string |
|||
. plotHeatmap |
||||
. . interpolationMethod |
string |
|||
. . plotType |
string |
|||
. . colorMap |
string |
|||
. . alpha |
number |
|||
. . extra |
string |
|||
peak_calling |
yes |
|||
. macs2 |
||||
. . run |
boolean |
|||
. . qvalue |
number |
|||
. . regions |
string |
|||
. . broad_cutoff |
number |
|||
. . extra |
string |
|||
. htseq_deseq2 |
||||
. . run |
boolean |
|||
. . use_htseq_count |
boolean |
|||
. . mode |
string |
|||
. . feature |
string |
|||
. . extra |
string |
|||
. . DESeq2 |
||||
. . . cumulative_filter_out |
integer |
|||
. . . smallest_group |
integer |
|||
. . . alpha |
number |
|||
. . . fc |
number |
|||
. . . extra |
string |
|||
. genomic_blanket |
||||
. . run |
boolean |
|||
. . window_size |
integer |
|||
. . extra |
string |
Linting and formatting
Linting results
1Workflow version: v0.5.0
2Wrapper version: v3.10.2
3No validator found for JSON Schema version identifier 'http://json-schema.org/draft-06/schema#'
4Defaulting to validator for JSON Schema version 'https://json-schema.org/draft/2020-12/schema'
5Note that schema file may not be validated correctly.
6KeyError in file "/tmp/tmpng2gjc13/niekwit-chip-seq-0d27612/workflow/scripts/general_functions.smk", line 40:
7'sample'
8 File "/tmp/tmpng2gjc13/niekwit-chip-seq-0d27612/workflow/Snakefile", line 42, in <module>
9 File "/tmp/tmpng2gjc13/niekwit-chip-seq-0d27612/workflow/scripts/general_functions.smk", line 40, in samples
10 File "/home/runner/work/snakemake-workflow-catalog/snakemake-workflow-catalog/.pixi/envs/default/lib/python3.13/site-packages/pandas/core/frame.py", line 4113, in __getitem__
11 File "/home/runner/work/snakemake-workflow-catalog/snakemake-workflow-catalog/.pixi/envs/default/lib/python3.13/site-packages/pandas/core/indexes/base.py", line 3819, in get_loc
Formatting results
1[DEBUG]
2[DEBUG] In file "/tmp/tmpng2gjc13/niekwit-chip-seq-0d27612/workflow/rules/trim.smk": Formatted content is different from original
3[DEBUG]
4[DEBUG] In file "/tmp/tmpng2gjc13/niekwit-chip-seq-0d27612/workflow/rules/align.smk": Formatted content is different from original
5[DEBUG]
6[DEBUG] In file "/tmp/tmpng2gjc13/niekwit-chip-seq-0d27612/workflow/rules/bigwig.smk": Formatted content is different from original
7[DEBUG]
8[DEBUG] In file "/tmp/tmpng2gjc13/niekwit-chip-seq-0d27612/workflow/rules/qc.smk": Formatted content is different from original
9[DEBUG]
10[DEBUG] In file "/tmp/tmpng2gjc13/niekwit-chip-seq-0d27612/workflow/rules/peaks.smk": Formatted content is different from original
11[DEBUG]
12[DEBUG] In file "/tmp/tmpng2gjc13/niekwit-chip-seq-0d27612/workflow/rules/deeptools.smk": Formatted content is different from original
13[DEBUG]
14[DEBUG] In file "/tmp/tmpng2gjc13/niekwit-chip-seq-0d27612/workflow/Snakefile": Formatted content is different from original
15[DEBUG]
16[DEBUG] In file "/tmp/tmpng2gjc13/niekwit-chip-seq-0d27612/workflow/rules/resources.smk": Formatted content is different from original
17[DEBUG]
18[DEBUG] In file "/tmp/tmpng2gjc13/niekwit-chip-seq-0d27612/workflow/rules/plotting.smk": Formatted content is different from original
19[INFO] 9 file(s) would be changed 😬
20
21snakefmt version: 0.11.5