Workflow: viralrecon.nanopore.cwl
Fetched 2026-06-24 02:47:59 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
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 |
../tool/quast/quast.cwl
(CommandLineTool)
|
||
| viralrecon |
viralrecon.nanopore.single.cwl
(Workflow)
|
||
| snpeff.build |
../tool/snpeff/snpeff.build.cwl
(CommandLineTool)
|
||
| get_primer_scheme |
viralrecon.nanopore.cwl#get_primer_scheme/0598472c-f9b1-4328-ac98-66248d613d32
(CommandLineTool)
|
||
| get_annotation_gff |
viralrecon.nanopore.cwl#get_annotation_gff/7620836b-d83f-41a7-ab20-4a3fe40c7d97
(CommandLineTool)
|
||
| get_reference_fasta |
viralrecon.nanopore.cwl#get_reference_fasta/d796b741-dae9-46fb-ac93-91b637b1fc36
(CommandLineTool)
|
||
| get_nextclade_dataset |
viralrecon.nanopore.cwl#get_nextclade_dataset/309dd535-20eb-47e4-81f2-dea60f9bf67d
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| quast.dir | Directory | ||
| snpsift.out | File[] | ||
| nanoplot.all | 6aa3a118d4fc9b3f570164094f9cccbf[] | ||
| pangolin.csv | File[] | ||
| nextclade.out | Directory[] | ||
| bcftoos.stats.txt | File[] | ||
| mosdepth.genome.all | 757f6d3990f4e973a79dc2e1b226abce[] | ||
| mosdepth.amplicon.all | 62c7969f558eb168df323ba29a70e547[] |
Permalink:
https://w3id.org/cwl/view/git/344088271e5f85632f2f8fdeae78af56089904a9/nanopore/workflow/viralrecon.nanopore.cwl
