viralrecon.nanopore.packed.cwl#main - Common Workflow Language Viewer

Workflow: viralrecon.nanopore.packed.cwl#main

Fetched 2026-09-30 01:07:44 GMT

Verified with cwltool version 3.1.20230201224320

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This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
GENOME_VERSION	String
FAST5_DIRECTORY	Directory
FASTQ_DIRECTORY	Directory
LIST_SAMPLE_NAME	String[]
LIST_BARCODE_NAME	String[]
SEQUENCING_SUMMARY	File
REFERENCE_FASTA_URL	String
ANNOTATION_GFF_GZ_URL	String
NEXTCLADE_TARBALL_URL	String

Steps

ID	Runs	Label	Doc
quast	viralrecon.nanopore.packed.cwl#quast.cwl (CommandLineTool)
viralrecon	viralrecon.nanopore.packed.cwl#viralrecon.nanopore.single.cwl (Workflow)
snpeff.build	viralrecon.nanopore.packed.cwl#snpeff.build.cwl (CommandLineTool)
get_primer_scheme	viralrecon.nanopore.packed.cwl#main/get_primer_scheme/a6f52aa1-8f64-46ad-a972-13cc151d446a (CommandLineTool)
get_annotation_gff	viralrecon.nanopore.packed.cwl#main/get_annotation_gff/3a453825-eb7c-4dbf-9d55-c9cfe3d48910 (CommandLineTool)
get_reference_fasta	viralrecon.nanopore.packed.cwl#main/get_reference_fasta/58a8b88e-3c0d-4be2-9bc8-54d935cb4526 (CommandLineTool)
get_nextclade_dataset	viralrecon.nanopore.packed.cwl#main/get_nextclade_dataset/05d11223-525b-4759-9c79-50c00ff92de1 (CommandLineTool)

Outputs

ID	Type	Label	Doc
quast.dir	Directory
snpsift.out	File[]
nanoplot.all	88ef4f82f5be2b189b71d342383c3e4b[]
pangolin.csv	File[]
nextclade.out	Directory[]
bcftoos.stats.txt	File[]
mosdepth.genome.all	73a14ab7f1809069269c6c6a1be1c27d[]
mosdepth.amplicon.all	fbe960a9b651a7ca8ffebabd3e28a106[]

Permalink:

https://w3id.org/cwl/view/git/344088271e5f85632f2f8fdeae78af56089904a9/nanopore/workflow/viralrecon.nanopore.packed.cwl?part=main