subworkflows/fastq_align_bamcmp_bwa
Align reads to two different reference genomes using bwa, then use bamcmp to keep only reads that align better to the first genome, then sort with samtools
bamcrambamcmpcontaminationalign
Description
Align reads to two different reference genomes using bwa, then use bamcmp to keep only reads that align better to the first genome, then sort with samtools
Input
Name (Type)
Description
Pattern
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
Structure: [ val(meta), [ path(reads) ] ]
BWA genome index files for the primary species.
Structure: [ val(meta2), path(primary_index) ]
BWA genome index files for the contamination species.
Structure: [ val(meta3), path(contaminant_index) ]
