SMURFsnake

SMURFSeq pipeline for CNV-analysis of Nanopore as Snakemake pipeline within a Singularity container

Set-up

• Update config.yaml with correct paths for reference genomes. Use expressive tags, i.e., hg19 and hg38, to designate the choices. Tags may be added or removed, keep in mind that they will become part of the output filenames.

ref: 
    hg19: path/to/reference/hg19.fa
    hg38: path/to/reference/hg38.fa.masked

• The remaining paths in the config.yaml point to directories within the Singularity container. If you choose to run the pipeline without the image, the required scripts and binning-files are located in the SMURFSeq.zip within the rebuild directory. Alternatively, the files may be obtained from the original source at smithlabcode.

• Construction of the singularity image requires a Unix machine with sudo rights and the singularity library in version >= 1.6. Additional information is provided by the ReadMe located in the rebuild directory.

• The file pipeline.bash contains the Snakemake execution command

Run as job on a cluster

Put the following line in the cluster-script to run pipeline as intended.

singularity exec --cleanenv SMURFsnake.sif bash pipeline.bash

# Code in pipeline.bash - Syntax is {sample}_{reference}_{bin_size}
snakemake --cores <INT> results/cnvs/{sample}_{reference}_{bin_size}.pdf

Run in shell

singularity shell --cleanenv SMURFsnake.sif