Workflow: wf_rnaediting2strands.cwl
Fetched 2023-01-11 10:47:21 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 | ||
| gtfdb | File | ||
| non_ag | Integer | ||
| species | String | ||
| input_bam | File | ||
| known_snp | File | ||
| reference | File | ||
| single_end | Boolean | ||
| chrom_sizes | File | ||
| edge_mutation | Integer | ||
| edit_fraction | Float | ||
| fwd_is_reverse | Boolean | ||
| rev_is_reverse | Boolean | ||
| keep_all_edited | Boolean | ||
| junction_overhang | Integer | ||
| min_variant_coverage | Integer | ||
| skip_duplicate_removal | Boolean | ||
| reverse_stranded_library | Boolean |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fwd |
rnaediting1strand.cwl
(Workflow)
|
||
| rev |
rnaediting1strand.cwl
(Workflow)
|
||
| step_calmd |
samtools-calmd.cwl
(CommandLineTool)
|
||
| index_reads |
samtools-index.cwl
(CommandLineTool)
|
samtools-index.cwl is developed for CWL consortium |
|
| split_strands |
split_strands.cwl
(CommandLineTool)
|
||
| step_annotator |
annotator.cwl
(CommandLineTool)
|
||
| step_score_edits |
score_edits_total_coverage.cwl
(CommandLineTool)
|
||
| step_combine_and_reformat |
combine_and_reformat.cwl
(CommandLineTool)
|
||
| step_bam_to_bigwig_forward |
wf_bam_to_bigwig.cwl
(Workflow)
|
||
| step_bam_to_bigwig_reverse |
wf_bam_to_bigwig.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| fwd_bigwig | File | ||
| rev_bigwig | File | ||
| scored_edits | File | ||
| combined_bedfile | File | ||
| annotated_bedfile | File | ||
| fwd_mpileup_output | File | ||
| rev_mpileup_output | File | ||
| fwd_call_snvs_output | File | ||
| fwd_rmdup_bam_output | File | ||
| rev_call_snvs_output | File | ||
| rev_rmdup_bam_output | File | ||
| fwd_rank_edits_output | File | ||
| fwd_sorted_bam_output | File | ||
| rev_rank_edits_output | File | ||
| rev_sorted_bam_output | File | ||
| fwd_filtered_bam_output | File | ||
| rev_filtered_bam_output | File | ||
| fwd_rank_edits_output_bed | File | ||
| rev_rank_edits_output_bed | File | ||
| fwd_filter_variants_output | File | ||
| fwd_format_variants_output | File | ||
| rev_filter_variants_output | File | ||
| rev_format_variants_output | File | ||
| fwd_filter_known_snp_output | File | ||
| rev_filter_known_snp_output | File |
Permalink:
https://w3id.org/cwl/view/git/5eb7864dd3622552dc95a927d3eb6ccf5f107745/cwl/wf_rnaediting2strands.cwl
