Produces a contamination report from FastQ input after subsampling
ch_reads
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
Structure: [ val(meta), path(reads) ]
sample_size
Number of reads to subsample for contamination detection.
kraken2_db
Kraken2 database used for contamination screening.
reports
Kraken2 contamination report.
Structure: [ val(meta), path(report) ]
*.txt
reads
Subsampled FastQ files as produced by seqtk sample.
*.fastq.gz
