nf-core/kmermaid
Version 1

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/ \
--readpairs 's3://olgabot-maca/sra/homosapiens/smartseq2quartzseq/{R1,R2}.fastq.gz,s3://olgabot-maca/sra/daniorerio/smart-seq/wholekidneymarrow_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 'possortedgenomebam.bam'

help Creators and Submitter
Creator
  • Olga Botvinnik
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Views: 256   Downloads: 6

Created: 25th Feb 2020 at 11:08

Last updated: 25th Feb 2020 at 15:19

Last used: 28th Sep 2020 at 08:04

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