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: 362   Downloads: 17

Created: 25th Feb 2020 at 11:08

Last updated: 25th Feb 2020 at 15:19

Last used: 15th Jan 2021 at 09:49

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

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