Workflow: viralrecon.nanopore.packed.cwl#viralrecon.nanopore.single.cwl
Fetched 2025-12-24 05:45:13 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 |
|---|---|---|---|
| SAMPLE_NAME | String | ||
| BARCODE_NAME | String | ||
| SNPEFF_CONFIG | File | ||
| SNPEFF_DATADIR | Directory | ||
| FAST5_DIRECTORY | Directory | ||
| FASTQ_DIRECTORY | Directory | ||
| SCHEME_DIRECTORY | Directory | ||
| NEXTCLADE_DATASET | Directory | ||
| SEQUENCING_SUMMARY | File | ||
| REFERENCE_GENOME_PREFIX | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| pigz |
viralrecon.nanopore.packed.cwl#pigz.cwl
(CommandLineTool)
|
||
| tabix |
viralrecon.nanopore.packed.cwl#tabix.cwl
(CommandLineTool)
|
||
| snpeff |
viralrecon.nanopore.packed.cwl#snpeff.cwl
(CommandLineTool)
|
||
| snpsift |
viralrecon.nanopore.packed.cwl#snpsift.cwl
(CommandLineTool)
|
||
| vcfuniq |
viralrecon.nanopore.packed.cwl#vcfuniq.cwl
(CommandLineTool)
|
||
| nanoplot |
viralrecon.nanopore.packed.cwl#nanoplot.cwl
(CommandLineTool)
|
||
| pangolin |
viralrecon.nanopore.packed.cwl#pangolin.cwl
(CommandLineTool)
|
||
| nextclade |
viralrecon.nanopore.packed.cwl#nextclade.cwl
(CommandLineTool)
|
||
| artic.minion |
viralrecon.nanopore.packed.cwl#artic.minion.cwl
(CommandLineTool)
|
||
| samtools.view |
viralrecon.nanopore.packed.cwl#samtools.view.cwl
(CommandLineTool)
|
||
| bcftools.stats |
viralrecon.nanopore.packed.cwl#bcftools.stats.cwl
(CommandLineTool)
|
||
| artic.guppyplex |
viralrecon.nanopore.packed.cwl#artic.guppyplex.cwl
(CommandLineTool)
|
||
| mosdepth.genome |
viralrecon.nanopore.packed.cwl#mosdepth.genome.cwl
(CommandLineTool)
|
||
| mosdepth.amplicon |
viralrecon.nanopore.packed.cwl#mosdepth.amplicon.cwl
(CommandLineTool)
|
||
| to_vcf_with_index |
viralrecon.nanopore.packed.cwl#viralrecon.nanopore.single.cwl/to_vcf_with_index/67efc14e-ef35-440f-bfa6-c90863b0b752
(CommandLineTool)
|
||
| extract_primer_bed |
viralrecon.nanopore.packed.cwl#viralrecon.nanopore.single.cwl/extract_primer_bed/00a73591-4533-4b51-80ce-3e518df8627d
(CommandLineTool)
|
||
| collapse_primer_bed |
viralrecon.nanopore.packed.cwl#collapse_primer_bed.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| snpsift.out | File | ||
| nanoplot.all | Directory[] | ||
| pangolin.csv | File | ||
| nextclade.out | Directory | ||
| consensus_fasta | File | ||
| bcftoos.stats.txt | File | ||
| mosdepth.genome.all | Directory[] | ||
| mosdepth.amplicon.all | Directory[] |
Permalink:
https://w3id.org/cwl/view/git/344088271e5f85632f2f8fdeae78af56089904a9/nanopore/workflow/viralrecon.nanopore.packed.cwl?part=viralrecon.nanopore.single.cwl
