Workflow: main-NA24385-sv.cwl
Fetched 2023-01-12 16:30:26 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| files | a56bc5725f8a6f6279466f8edc596f22[] | ||
| analysis | String[] | ||
| resources | String[] | ||
| description | String[] | ||
| rgnames__lb | String[] | ||
| rgnames__pl | String[] | ||
| rgnames__pu | String[] | ||
| rgnames__rg | String[] | ||
| genome_build | String[] | ||
| rgnames__lane | String[] | ||
| metadata__batch | String[] | ||
| rgnames__sample | String[] | ||
| reference__twobit | File[] | ||
| metadata__phenotype | String[] | ||
| config__algorithm__qc | ee35f4d1bf9c9c3ceedcdaf7f4a9642b[] | ||
| reference__fasta__base | File[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__adapters | d906ae065f6b6ba1300583eec7c8e869[] | ||
| config__algorithm__coverage | File[] | ||
| config__algorithm__svcaller | c11a9c432c097223da00e8a07b773b10[] | ||
| config__algorithm__tools_on | 9f66969381d05cbb4d000d821af417b3[] | ||
| config__algorithm__bam_clean | Boolean[] | ||
| config__algorithm__tools_off | b72397159051edc7d374a2b016101832[] | ||
| reference__minimap2__indexes | 4723ce9d3eb6f6725c49e24281929494[] | ||
| reference__snpeff__GRCh37_75 | File[] | ||
| config__algorithm__svvalidate | File[] | ||
| config__algorithm__trim_reads | Boolean[] | ||
| config__algorithm__recalibrate | Boolean[] | ||
| genome_resources__variation__lcr | File[] | ||
| genome_resources__aliases__snpeff | String[] | ||
| config__algorithm__exclude_regions | 81409aec3e872abb033d5aff9e8327f6[] | ||
| config__algorithm__mark_duplicates | Boolean[] | ||
| config__algorithm__variant_regions | File[] | ||
| genome_resources__rnaseq__gene_bed | File[] | ||
| genome_resources__variation__dbsnp | File[] | ||
| genome_resources__variation__polyx | File[] | ||
| config__algorithm__align_split_size | Boolean[] | ||
| config__algorithm__nomap_split_size | Long[] | ||
| config__algorithm__coverage_interval | String[] | ||
| config__algorithm__nomap_split_targets | Long[] | ||
| genome_resources__variation__encode_blacklist | File[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| svcall |
wf-svcall.cwl
(Workflow)
|
||
| alignment |
wf-alignment.cwl
(Workflow)
|
||
| qc_to_rec |
steps/qc_to_rec.cwl
(CommandLineTool)
|
||
| batch_for_sv |
steps/batch_for_sv.cwl
(CommandLineTool)
|
||
| prep_samples |
steps/prep_samples.cwl
(CommandLineTool)
|
||
| summarize_sv |
steps/summarize_sv.cwl
(CommandLineTool)
|
||
| multiqc_summary |
steps/multiqc_summary.cwl
(CommandLineTool)
|
||
| alignment_to_rec |
steps/alignment_to_rec.cwl
(CommandLineTool)
|
||
| pipeline_summary |
steps/pipeline_summary.cwl
(CommandLineTool)
|
||
| calculate_sv_bins |
steps/calculate_sv_bins.cwl
(CommandLineTool)
|
||
| prep_samples_to_rec |
steps/prep_samples_to_rec.cwl
(CommandLineTool)
|
||
| calculate_sv_coverage |
steps/calculate_sv_coverage.cwl
(CommandLineTool)
|
||
| normalize_sv_coverage |
steps/normalize_sv_coverage.cwl
(CommandLineTool)
|
||
| postprocess_alignment |
steps/postprocess_alignment.cwl
(CommandLineTool)
|
||
| combine_sample_regions |
steps/combine_sample_regions.cwl
(CommandLineTool)
|
||
| postprocess_alignment_to_rec |
steps/postprocess_alignment_to_rec.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| align_bam | File[] | ||
| sv__calls | c5856a6d51a8292e4abb1542e9e3b5bd[] | ||
| summary__multiqc | File[] | ||
| rgnames__sample_out | String[] | ||
| regions__sample_callable | File[] | ||
| svvalidate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/a297e87e014de998b8df9c90700c29173ec09932/NA24385-sv/NA24385-sv-workflow/main-NA24385-sv.cwl
