nf-kmer-similarity

This is a Nextflow workflow for running k-mer similarity

Usage

With a samples.csv file:

nextflow run czbiohub/nf-kmer-similarity --outdir s3://olgabot-maca/nf-kmer-similarity/ --samples samples.csv

With R1, R2 read pairs:

nextflow run czbiohub/nf-kmer-similarity --outdir s3://olgabot-maca/nf-kmer-similarity/ \

--readpairs 's3://olgabot-maca/sra/homosapiens/smartseq2quartzseq/{R1,R2}.fastq.gz,s3://olgabot-maca/sra/daniorerio/smart-seq/wholekidneymarrow_prjna393431/*{1,2}.fastq.gz'

...