Workflows
What is a Workflow?Filters
Workflow converts one or multiple bam/cram files to fastq format
CAGE-seq pipeline
Type: Nextflow
Creators: Kevin Menden, Tristan Kast, Matthias Hörtenhuber
Submitter: WorkflowHub Sandbox Bot
Simple bacterial assembly and annotation
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
B and T cell repertoire analysis pipeline with the Immcantation framework.
Type: Nextflow
Creators: Gisela Gabernet, Susanna Marquez, Alexander Peltzer, Simon Heumos
Submitter: WorkflowHub Sandbox Bot
nf-kmer-similarity
This is a Nextflow workflow for running k-mer similarity
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' ...
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