Docker.md

Docker workflow

We provide an image (mosaicatcher-pipeline-hg38) that contains all software as well as the reference genome hg38.

This can be used to easily run the MosaiCatcher workflow on own samples.

Requirements

• Docker (tested with version 18.09)
• A bam folder containing Strand-seq BAM file (as described in Setup)
• Optionally, a folder with VCF files (as described in SNV calls for haplotype separation)

How to run

To add your own data, just mount the respective volumes into the /pipeline directory of the Docker container. Here is an example (you need to replace the /path/to part):

sudo docker run -ti \
    -v /path/to/bam/:/pipeline/bam/ \
    -v /path/to/sv_calls/:/pipeline/sv_calls/ \
    -v /path/to/postprocessing/:/pipeline/postprocessing/ \
    smei/mosaicatcher-pipeline-hg38 \
    bash
root@04f2b2aeb86c:/pipeline#

Note that the folders sv_calls and postprocessing are necessary to store the result files permanently. Otherwise, you can also copy them to the bam folder after the pipeline has finished

Then, within the container, you potentially want to change Snake.config-singularity.json (for example to specify that your reads are single-ended, or to tell the pipeline that you would like to use a custom SNV call set).

To start the pipeline, simply type

snakemake --configfile Snake.config-singularity.json