Nextflow pipeline for normalizing fastq reads

This is nextflow wrapper to run bbmap.sh. It's inception was to normalize fastq file from monkeypox sequencing. It could be used for other purposes.

Input

A folder containing paired end fastq files

Output

A folder containing depth normalized fastq files.

Process

graph TD;
A[Sequence files]-->B[Normalized sequence files]
D[Sequence files]-->E[Normalized sequence files]

Loading

Typical command

nextflow run BCCDC-PHL/bbmap-nf --input_fastq [directory containing fastqs] --outdir [directory for output] -profile conda --cache ~/.conda/envs -with-report report.html