xin-huang/selscape
Snakemake Workflow for Investigating Genomic Landscapes of Natural Selection
Overview
Latest release: v1.0.0, Last update: 2026-05-16
Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=xin-huang/selscape
Quality control: linting: failed formatting: failed
Topics: balancing-selection distribution-of-fitness-effects natural-selection population-genomics positive-selection
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/xin-huang/selscape . --tag v1.0.0
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 using apptainer/singularity, use
snakemake --cores all --sdm apptainer
To run the workflow using a combination of conda and apptainer/singularity for software deployment, use
snakemake --cores all --sdm conda apptainer
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.
Configuration
Please use the template main.yaml, selscan.yaml, scikit-allel.yaml, betascan.yaml, and dadi-cli.yaml to customize the workflow to your dataset. Configuration instructions can be found in the Configuration section of the manual.
Workflow parameters
The following table is automatically parsed from the workflow’s config.schema.y(a)ml file.
Parameter |
Type |
Description |
Required |
Default |
|---|---|---|---|---|
species |
string |
Species name |
yes |
|
tax_id |
integer |
NCBI taxonomy ID |
yes |
|
ref_genome |
string |
Reference genome build (e.g., hg38) |
yes |
|
anc_alleles |
[‘object’, ‘null’] |
Ancestral allele information for polarization |
||
. path |
string |
Base folder for ancestral allele information |
||
. prefix |
string |
Ancestral allele information filename prefix |
||
genome_annotation |
string |
Path to genome annotation GTF file |
||
gene2go |
string |
Path to gene2go mapping file |
||
hwe_pvalue |
number |
Hardy-Weinberg equilibrium p-value threshold |
yes |
0.001 |
rmsk |
[‘string’, ‘null’] |
Path to repeat masker BED file |
||
seg_dup |
[‘string’, ‘null’] |
Path to segmental duplications BED file |
||
sim_rep |
[‘string’, ‘null’] |
Path to simple repeats BED file |
||
ploidy |
integer |
Organism ploidy |
yes |
|
populations |
array |
List of population IDs to analyze |
yes |
|
data_folder |
string |
Base folder for input VCF files |
yes |
|
vcf_prefix |
string |
VCF filename prefix |
yes |
|
vcf_suffix |
string |
VCF filename suffix |
yes |
|
metadata |
string |
Path to sample metadata file |
yes |
|
chromosomes |
array |
List of chromosomes to analyze |
yes |
|
betascan_config |
string |
Path to BetaScan configuration file |
yes |
|
selscan_config |
string |
Path to selscan configuration file |
yes |
|
dadi_config |
string |
Path to dadi-cli configuration file |
yes |
|
scikit_allel_config |
string |
Path to scikit-allel configuration file |
yes |
Linting and formatting
Linting results
1KeyError in file "/tmp/tmp6r6w02sz/xin-huang-selscape-129efc2/workflow/rules/common.smk", line 33:
2'selscan_config'
3 File "/tmp/tmp6r6w02sz/xin-huang-selscape-129efc2/workflow/rules/common.smk", line 33, in <module>
Formatting results
1[DEBUG]
2[DEBUG] In file "/tmp/tmp6r6w02sz/xin-huang-selscape-129efc2/workflow/rules/5.2_balancing_selection_scikit-allel.smk": Formatted content is different from original
3[DEBUG]
4[DEBUG] In file "/tmp/tmp6r6w02sz/xin-huang-selscape-129efc2/workflow/rules/4.1_positive_selection_selscan.smk": Formatted content is different from original
5[DEBUG]
6[DEBUG] In file "/tmp/tmp6r6w02sz/xin-huang-selscape-129efc2/workflow/rules/2_preprocess.smk": Formatted content is different from original
7[DEBUG]
8[DEBUG] In file "/tmp/tmp6r6w02sz/xin-huang-selscape-129efc2/workflow/rules/4.4_positive_selection_scikit-allel_xp.smk": Formatted content is different from original
9[DEBUG]
10[DEBUG] In file "/tmp/tmp6r6w02sz/xin-huang-selscape-129efc2/workflow/rules/5.1_balancing_selection_betascan.smk": Formatted content is different from original
11[DEBUG]
12[DEBUG]
13[DEBUG] In file "/tmp/tmp6r6w02sz/xin-huang-selscape-129efc2/workflow/rules/4.3_positive_selection_scikit-allel.smk": Formatted content is different from original
14[DEBUG]
15[DEBUG] In file "/tmp/tmp6r6w02sz/xin-huang-selscape-129efc2/workflow/rules/3_polarization.smk": Formatted content is different from original
16[DEBUG]
17[DEBUG] In file "/tmp/tmp6r6w02sz/xin-huang-selscape-129efc2/workflow/rules/common.smk": Formatted content is different from original
18[DEBUG]
19<unknown>:2: SyntaxWarning: invalid escape sequence '\('
20[DEBUG] In file "/tmp/tmp6r6w02sz/xin-huang-selscape-129efc2/workflow/rules/6_deleterious_dfe_dadi.smk": Formatted content is different from original
21[DEBUG]
22[DEBUG] In file "/tmp/tmp6r6w02sz/xin-huang-selscape-129efc2/workflow/Snakefile": Formatted content is different from original
23[DEBUG]
24[DEBUG] In file "/tmp/tmp6r6w02sz/xin-huang-selscape-129efc2/workflow/rules/4.2_positive_selection_selscan_xp.smk": Formatted content is different from original
25[INFO] 11 file(s) would be changed 😬
26[INFO] 1 file(s) would be left unchanged 🎉
27
28snakefmt version: 0.11.5