merge_samplesheets

This program is a wrapper for Jeff Bailey's mipscripts_v0dev2.py sample sheet merger program. If you have sequenced MIP samples multiple times (via resequencing or recapturing) and your goal is to merge these datasets together (collecting all the data associated with e.g. sample 2 in run 1 and sample 2 in run 2 into a single sample 2 file), this program allows these types of mergers. Input is a group of sample sheets (each containing a corresponding fastq subfolders). Output is a single sample sheet that has a single merged fastq subfolder.

Installation:

• Install mambaforge: https://github.com/conda-forge/miniforge#mambaforge
• Create a mamba environment and install snakemake there:

mamba create -c conda-forge -c bioconda -n snakemake snakemake

Setup your environment:

• Change directory to a folder where you want to run the analysis
• Download the merge_samplesheets.smk file into this folder
• Download the merge_samplesheets.yaml file into the same folder

Usage:

• Edit the config.yaml file using the instructions in the comments. Use a text editor that outputs unix line endings (e.g. vscode, notepad++, gedit, micro, emacs, vim, vi, etc.)
• If snakemake is not your active conda environment, activate snakemake with:

mamba activate snakemake

• Run snakemake with:

snakemake -s merge_samplesheets.smk --cores [your_desired_core_count]

Help:

For additional help on Jeff's merge script, try running this command (assuming you have access to a computer that is part of the bailey lab group): python3 /nfs/jbailey5/baileyweb/bailey_share/bin/mipscripts_v0dev2.py merge_sampleset -h