wisekh6 / valibam

Minimal nextflow pipeline to check integrity of BAM files with various tools and to generate the checksum (md5) of each files.

---------  Under construction!  ---------

valibam

Minimal nextflow pipeline to check integrity of BAM files with various tools and to generatemd5sum of the files.

Quick Start

Required Arguments:

argument	value
inputdir	a path to the input folder with bam files to be checked
outdir	a path to an output folder for the .txt summary report files. The reports will be in the outdir/Results/folder
ref	a path to the fasta file used as a reference genome for mapping the bam files

To test the pipeline with the example input you can run:

# Clone the repository
git clone https://github.com/cgpu/ValidateBAM-nf.git

# cd into the repo folder 
cd merge-bams-nf

# Execute nextflow run command with example input parameters
nextflow run merge-bams-nf/main.nf --inputdir path/to/input/folder/ --tool 'samtools'