Workflow: animal-genome-assembly.packed.cwl#hybrid_error_correction.cwl
Fetched 2024-05-08 05:37:52 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)
- 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 |
|---|---|---|---|
| THREADS | Integer | ||
| INPUT_FASTA | File | ||
| INPUT_SHORTREAD | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| pilon |
animal-genome-assembly.packed.cwl#pilon.cwl
(CommandLineTool)
|
Pilon for hybrid genome assembly |
|
| bwa-mem |
animal-genome-assembly.packed.cwl#bwa-mem.cwl
(CommandLineTool)
|
string |
|
| bwa-index |
animal-genome-assembly.packed.cwl#bwa-index.cwl
(CommandLineTool)
|
string |
|
| samtools-sort |
animal-genome-assembly.packed.cwl#samtools-sort.cwl
(CommandLineTool)
|
samtools sort, sort given bam file |
|
| samtools-view |
animal-genome-assembly.packed.cwl#samtools-view.cwl
(CommandLineTool)
|
samtools view to convert sam format to bam format |
|
| samtools-index |
animal-genome-assembly.packed.cwl#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/6db4456ca7314b036e59f50910654066da99772a/workflow/animal-genome-assembly/animal-genome-assembly.packed.cwl?part=hybrid_error_correction.cwl
