Workflow: rnaediting1strand.cwl
Fetched 2023-01-11 11:07:57 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 3-clause "New" or "Revised" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| ct | Boolean | ||
| dp | String | ||
| gt | Boolean | ||
| beta | Integer | ||
| alpha | Integer | ||
| non_ag | Integer | ||
| known_snp | File | ||
| reference | File | ||
| single_end | Boolean | ||
| edge_mutation | Integer | ||
| edit_fraction | Float | ||
| variants_only | Boolean | ||
| keep_all_edited | Boolean | ||
| junction_overhang | Integer | ||
| reverse_split_bam | Boolean | ||
| input_unsorted_bam | File | ||
| min_variant_coverage | Integer | ||
| skip_duplicate_removal | Boolean | ||
| reverse_stranded_library | Boolean |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sort |
sort.cwl
(CommandLineTool)
|
||
| rmdup |
rmdup.cwl
(CommandLineTool)
|
||
| mpileup |
mpileup.cwl
(CommandLineTool)
|
||
| call_snvs |
call_snvs.cwl
(CommandLineTool)
|
||
| rank_edits |
rank_edits.cwl
(CommandLineTool)
|
||
| index_reads |
samtools-index.cwl
(CommandLineTool)
|
samtools-index.cwl is developed for CWL consortium |
|
| filter_reads |
filter_reads.cwl
(CommandLineTool)
|
||
| filter_variants |
filter_variants.cwl
(CommandLineTool)
|
||
| format_variants |
format_variants.cwl
(CommandLineTool)
|
||
| filter_known_snp |
filter_known_snp.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| mpileup_output | File | ||
| call_snvs_output | File | ||
| rmdup_bam_output | File | ||
| rank_edits_output | File | ||
| sorted_bam_output | File | ||
| filtered_bam_output | File | ||
| rank_edits_output_bed | File | ||
| filter_variants_output | File | ||
| format_variants_output | File | ||
| filter_known_snp_output | File |
Permalink:
https://w3id.org/cwl/view/git/5eb7864dd3622552dc95a927d3eb6ccf5f107745/cwl/rnaediting1strand.cwl
