Workflow: hybrid_error_correction.cwl
Fetched 2023-01-04 16:14:51 GMT
Verified with cwltool version 3.1.20221201130942
Sub workflow used in the Animal Genome Assembly pipeline by Kazuharu Arakawa (@gaou_ak), CWLized by Tazro Ohta (@inutano)
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- |
- Default Values
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- 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 |
|---|---|---|---|
| THREADS | Integer | ||
| INPUT_FASTA | File | ||
| INPUT_SHORTREAD | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| pilon |
../../tool/pilon/pilon.cwl
(CommandLineTool)
|
Pilon for hybrid genome assembly |
|
| bwa-mem |
../../tool/bwa/mem/bwa-mem.cwl
(CommandLineTool)
|
string |
|
| bwa-index |
../../tool/bwa/index/bwa-index.cwl
(CommandLineTool)
|
string |
|
| samtools-sort |
../../tool/samtools/sort/samtools-sort.cwl
(CommandLineTool)
|
samtools sort, sort given bam file |
|
| samtools-view |
../../tool/samtools/view/samtools-view.cwl
(CommandLineTool)
|
samtools view to convert sam format to bam format |
|
| samtools-index |
../../tool/samtools/index/samtools-index.cwl
(CommandLineTool)
|
samtools index to create index for given bam file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| fasta | File |
Permalink:
https://w3id.org/cwl/view/git/0cd20e1be620ae0817a1aa4286d73b78c89809f0/workflow/animal-genome-assembly/hybrid_error_correction.cwl
