command
» nextflow run nf-core/kmermaid -profile test
clones in last 5 months

487

stars

2

watchers

0

last release

N/A

last updated

2 days ago

open issues

11

pull requests

22

collaborators

get in touch

ask a question on Slack

open an issue on GitHub

Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Documentation

The nf-core/kmermaid pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting

Usage

With a samples.csv file:

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

With R1, R2 read pairs:

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

With fasta files:

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

Credits

nf-core/kmermaid was originally written by Olga Botvinnik.