abbyevewilliams/map-pipeline

A snakemake pipeline for mapping next generation sequencing reads from avian museum samples.

Overview

Topics:

Latest release: None, Last update: 2025-04-07

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/abbyevewilliams/map-pipeline . --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.

Configuring the workflow

You should configure the following options in the config/config.yaml:

  • reads_dir: the absolute path to your raw reads.

  • samples: the path to your samples.txt file. This should contain the base names of your samples, e.g. if you have reads sample1_1.fastq.gz and sample1_2.fastq.gz then you should add sample1 to the samples.txt (see template provided).

  • reference_genome: path to your reference genome.

  • run_fastp: [True/False] whether to run fastp with default settings to trim and remove adapters. You may choose to disable this if you have already cleaned your reads using a custom pipeline, or if you prefer to do QC after mapping.

  • dedup_with_picard: [True/False] whether to use PicardMarkDuplicates for duplicate removal. If using merged reads (a common output of ancient/historical DNA cleaning pipelines) you should disable this option, and DeDup will be used instead.

  • mapdamage_rescale: [True/False] whether to use Mapdamage2 to rescale base qualities. Set to true for historical samples.

Linting and formatting

Linting results

FileNotFoundError in file /tmp/tmp4bqdqnso/workflow/Snakefile, line 13:
[Errno 2] No such file or directory: '/data/biol-silvereye/ball6625/map-pipeline/config/zborb-samples.txt'
  File "/tmp/tmp4bqdqnso/workflow/Snakefile", line 13, in <module>

Formatting results

[DEBUG] 
[DEBUG] In file "/tmp/tmp4bqdqnso/workflow/rules/map.smk":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmp4bqdqnso/workflow/rules/damage.smk":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmp4bqdqnso/workflow/Snakefile":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmp4bqdqnso/workflow/rules/fastp.smk":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmp4bqdqnso/workflow/rules/fastqc.smk":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmp4bqdqnso/workflow/rules/clean.smk":  Formatted content is different from original
[INFO] 6 file(s) would be changed 😬

snakefmt version: 0.10.2