Workflow: main-NA24385-sv.cwl
Fetched 2023-01-12 03:56:24 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 | 3b9a79afcb959846d8074e4fc8d28c95[] | ||
| 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 | 0fa794991d11e331f28832e44777c684[] | ||
| reference__fasta__base | File[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__adapters | 25ff20e05fb0d1f8aa224fc73e9b4520[] | ||
| config__algorithm__coverage | File[] | ||
| config__algorithm__svcaller | 1f552fc530fed848b9042886603b5a20[] | ||
| config__algorithm__tools_on | 04421370a87e20cc2cea795354eb2152[] | ||
| config__algorithm__bam_clean | Boolean[] | ||
| config__algorithm__tools_off | 48e711e5ad5a8b1b2f0bf2669c45e611[] | ||
| reference__minimap2__indexes | 1b222accb3abdfb7ab457fec6a4c9144[] | ||
| 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 | fc3c23ae6aa10a2d320e2de06e5d1fe5[] | ||
| 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 | d4fca17a171f1c212b52c5ead059db40[] | ||
| summary__multiqc | File[] | ||
| rgnames__sample_out | String[] | ||
| regions__sample_callable | File[] | ||
| svvalidate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/afd674a6d64fb4e115c0b3fe95b7bb1b73ec69a9/NA24385-sv/NA24385-sv-workflow/main-NA24385-sv.cwl
