Bioinflows-Bioversity-CIAT/tm-shift_designer
A workflow intended to perform the design of tm-shift primers for genotype SNPs
Overview
Topics:
Latest release: v0.2.0, Last update: 2025-02-13
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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/Bioinflows-Bioversity-CIAT/tm-shift_designer . --tag v0.2.0
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.
To configure the workflow, modify config/config.yaml according to yout needs, following the explanations provided in the file.
Add assemblies to file config/assembly_units.txt. This file is tab-separated file with two columns: assembly_id and path. The former is the alias of the assembly and the latter the path of .fasta assembly file. Both columns are mandatory and cannot be duplicated.
Add target variants where you want to design the Tm-shit primers in the file config/target_variants.txt. This file is tab-sepparated. In the column variant_id specify a unique name to identify the variant. The assembly_id uses the assembly_id specified in config/assembly_units.txt and the columns chrom and pos define the physical position on the given assembly. In columns ref and alt is stored the reference and alternative allele that the primers going to genotype.
Linting and formatting
Linting results
None
Formatting results
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[DEBUG] In file "/tmp/tmpii8pckop/Bioinflows-Bioversity-CIAT-tm-shift_designer-25dbf3e/workflow/rules/primer_search.smk": Formatted content is different from original
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[DEBUG] In file "/tmp/tmpii8pckop/Bioinflows-Bioversity-CIAT-tm-shift_designer-25dbf3e/workflow/rules/primer_selection.smk": Formatted content is different from original
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[DEBUG] In file "/tmp/tmpii8pckop/Bioinflows-Bioversity-CIAT-tm-shift_designer-25dbf3e/workflow/rules/sequence_processing.smk": Formatted content is different from original
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[DEBUG] In file "/tmp/tmpii8pckop/Bioinflows-Bioversity-CIAT-tm-shift_designer-25dbf3e/workflow/Snakefile": Formatted content is different from original
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[DEBUG] In file "/tmp/tmpii8pckop/Bioinflows-Bioversity-CIAT-tm-shift_designer-25dbf3e/workflow/rules/common.smk": Formatted content is different from original
[INFO] 5 file(s) would be changed 😬
snakefmt version: 0.10.2