sequana-mapper 0.12.0

Installation

If you already have all requirements, you can install the packages using pip:

pip install sequana_mapper --upgrade

Otherwise, you can create a sequana_mapper conda environment executing:

conda env create -f environment.yml

and later activate the environment:

conda activate sequana_mapper

A third option is to install the pipeline with pip method (see above) and use singularity as explained afterwards.

Usage

sequana_mapper --input-directory DATAPATH  --mapper bwa --create-bigwig
sequana_mapper --input-directory DATAPATH  --mapper bwa --do-coverage

This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:

cd mapper
sh mapper.sh  # for a local run

This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters:

snakemake -s mapper.rules -c config.yaml --cores 4 --stats stats.txt

Or use sequanix interface.

Requirements

This pipelines requires the following executable(s):

• bamtools

• bwa

• multiqc

• sequana_coverage

• minimap2

• bowtie2

• deeptools

Details

This pipeline runs mapper in parallel on the input fastq files (paired or not). A brief sequana summary report is also produced. When using –pacbio option, -x map-pb options is automatically added to the config.yaml file and the readtag is set to None.

Rules and configuration details

Here is the latest documented configuration file to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.

Changelog

Contribute & Code of Conduct

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.