Workflow: main-NA24385-sv.cwl
Fetched 2023-01-12 08:38:16 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 | abb7a0373d87c3bfdeef328eb475d537[] | ||
| 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 | b2d2a52c4efa53c63103d9b58e897e2c[] | ||
| reference__fasta__base | File[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__adapters | 9a415ee2024be667b468f0de63cf0bf3[] | ||
| config__algorithm__coverage | File[] | ||
| config__algorithm__svcaller | e606e0f06c348c592fc86f6f44694734[] | ||
| config__algorithm__tools_on | 913866cc7f1773d7d27c69620c1bf29d[] | ||
| config__algorithm__bam_clean | Boolean[] | ||
| config__algorithm__tools_off | dbf08f52602299dea40bafd26fb782c3[] | ||
| reference__minimap2__indexes | e152ea84b30fdc17749be6ed0514e97a[] | ||
| 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 | 316cf2ed925814c6c3cbbcd69fe6d1de[] | ||
| 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 | 60c85cea153f29ea410b4d843f9a6305[] | ||
| summary__multiqc | File[] | ||
| rgnames__sample_out | String[] | ||
| regions__sample_callable | File[] | ||
| svvalidate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/24e9fff0d5e406323b826c0e8bd150be0ff8aba4/NA24385-sv/NA24385-sv-workflow/main-NA24385-sv.cwl
