dawidkrzeciesa/dna-seq-cnv

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Overview

Topics:

Latest release: None, Last update: 2023-08-30

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/dawidkrzeciesa/dna-seq-cnv . --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.

Please set the path to the directory containing the BAM files and the reference genome in the config.yaml file.

In the samples.tsv file, use the same sample names as in the dna-seq-varlociraptor pipeline, which was used for generating the bam files. The target_bed files for the libraries were downloaded from the manufacturer, Agilent.

Linting and formatting

Linting results

WorkflowError:
Workflow requires a total number of cores to be defined (e.g. because a rule defines its number of threads as a fraction of a total number of cores). Please set it with --cores N with N being the desired number of cores. Consider to use this in combination with --max-threads to avoid jobs with too many threads for your setup. Also make sure to perform a dryrun first.

Formatting results

[DEBUG] 
[DEBUG] In file "/tmp/tmpj6gic0hn/workflow/Snakefile":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmpj6gic0hn/workflow/rules/oncoprint.smk":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmpj6gic0hn/workflow/rules/common.smk":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmpj6gic0hn/workflow/rules/cnvkit.smk":  Formatted content is different from original
[INFO] 4 file(s) would be changed 😬

snakefmt version: 0.8.5