zigeuner/nf-commonreads

nextflow pipeline for finding common reads between two bam files

Simple Nextflow script to find reads common to two bam files

procedure:

• extract mapped reads into two derivative bam files: mapped1.bam and mapped2.bam
• extract read names and sort
• compare read names and find common read names using linux 'comm' utility
• extract reads from mapped1.bam using common read names and return common_mapped1.bam
• extract reads from mapped2.bam using common read names and return common_mapped2.bam

usage example:

nextflow run nf-commonreads/main.nf -with-docker [nextflow-image] --bam1 [path or s3 folder uri] --bam2 [path or s3 folder uri] --outdir [path to folder or s3 folder uri]

If the input bam filenames are not unique, then specify tags like this:

nextflow run nf-commonreads/main.nf -with-docker [nextflow-image] --bam1 [path or s3 folder uri] --tag1 [unique tag] --bam2 [path or s3 folder uri] --tag2 [unique tag] --outdir [path to folder or s3 folder uri]