nf-core/kmermaid
Version 1

Workflow Type: Nextflow

nf-kmer-similarity

This is a Nextflow workflow for running k-mer similarity

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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'

With bam file

nextflow run czbiohub/nf-kmer-similarity --outdir s3://olgabot-maca/nf-kmer-similarity/ \ --bam 'possorted_genome_bam.bam'

Total size: 112 KB
help Creators and Submitter
Creator
  • Olga Botvinnik
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Views: 815   Downloads: 24

Created: 25th Feb 2020 at 11:08

Last updated: 25th Feb 2020 at 15:19

Last used: 29th Nov 2021 at 04:43

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Version History

Version 1 (earliest) Created 25th Feb 2020 at 11:08 by Finn Bacall

Added/updated 35 files


Open master 3159dee

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