command
» nextflow run nf-core/kmermaid -profile test
clones in last 3 months

449

stars

0

watchers

0

last release

N/A

last updated

5 days ago

open issues

1

pull requests

9

collaborators

get in touch

ask a question on Slack

open an issue on GitHub

nf-kmer-similarity

This is a Nextflow workflow for running k-mer similarity

Docker Cloud Build Status

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'