README.md

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/ \
  --read_pairs 's3://olgabot-maca/sra/homo_sapiens/smartseq2_quartzseq/*{R1,R2}*.fastq.gz,s3://olgabot-maca/sra/danio_rerio/smart-seq/whole_kidney_marrow_prjna393431/*{1,2}.fastq.gz'

With SRA ids:

nextflow run czbiohub/nf-kmer-similarity --outdir s3://olgabot-maca/nf-kmer-similarity/ --sra SRP016501

With fasta files:

nextflow run czbiohub/nf-kmer-similarity --outdir s3://olgabot-maca/nf-kmer-similarity/ \
  --fastas '*.fasta'