Workflow: main-somatic.cwl
Fetched 2023-01-03 20:13:39 GMT
Verified with cwltool version 3.1.20221201130942
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- Nested Workflows
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- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| files | d04480650f89ea9630c04b8f639569d8[] | ||
| analysis | String[] | ||
| vrn_file | File[] | ||
| resources | String[] | ||
| description | String[] | ||
| rgnames__lb | String[] | ||
| rgnames__pl | String[] | ||
| rgnames__pu | String[] | ||
| rgnames__rg | String[] | ||
| genome_build | String[] | ||
| rgnames__lane | String[] | ||
| reference__rtg | File[] | ||
| metadata__batch | String[] | ||
| rgnames__sample | String[] | ||
| reference__twobit | File[] | ||
| metadata__phenotype | String[] | ||
| config__algorithm__qc | 566797ae2af873cbff1bd79dd3cc1a9d[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| reference__snpeff__hg19 | File[] | ||
| reference__genome_context | b4291a394975f55ffedd2ed386ed01ed[] | ||
| config__algorithm__aligner | Boolean[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__vcfanno | 0ec3673845e3c9dc8cb0c8f2da079ba3[] | ||
| config__algorithm__adapters | 9164bb1f30792ba318ae1dc40ed01b1b[] | ||
| config__algorithm__coverage | File[] | ||
| config__algorithm__ensemble | String[] | ||
| config__algorithm__tools_on | be6ec5044cd9715a9c54a517a8fcc7c0[] | ||
| config__algorithm__umi_type | String[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__bam_clean | Boolean[] | ||
| config__algorithm__tools_off | c5222bce61e0d531dbc3ff85a93c5824[] | ||
| reference__minimap2__indexes | a3a2bc4590d818fa843545b111042723[] | ||
| config__algorithm__trim_reads | Boolean[] | ||
| config__algorithm__recalibrate | Boolean[] | ||
| config__algorithm__variantcaller | ca00d6d69a2232cff4211e557f8cba7c[] | ||
| genome_resources__aliases__human | Boolean[] | ||
| genome_resources__variation__esp | File[] | ||
| genome_resources__variation__lcr | String[] | ||
| genome_resources__aliases__snpeff | String[] | ||
| genome_resources__variation__exac | File[] | ||
| config__algorithm__exclude_regions | a6fbc864b37a4a46cfb67bc84c9df35e[] | ||
| config__algorithm__mark_duplicates | Boolean[] | ||
| config__algorithm__variant_regions | File[] | ||
| genome_resources__aliases__ensembl | String[] | ||
| genome_resources__rnaseq__gene_bed | File[] | ||
| genome_resources__variation__1000g | File[] | ||
| genome_resources__variation__dbsnp | File[] | ||
| genome_resources__variation__polyx | String[] | ||
| config__algorithm__align_split_size | Long[] | ||
| config__algorithm__nomap_split_size | Long[] | ||
| config__algorithm__validate_regions | File[] | ||
| genome_resources__variation__cosmic | File[] | ||
| config__algorithm__coverage_interval | String[] | ||
| genome_resources__variation__clinvar | File[] | ||
| config__algorithm__min_allele_fraction | Double[] | ||
| config__algorithm__nomap_split_targets | Long[] | ||
| genome_resources__variation__train_hapmap | File[] | ||
| genome_resources__variation__train_indels | File[] | ||
| genome_resources__variation__encode_blacklist | String[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| alignment |
wf-alignment.cwl
(Workflow)
|
||
| qc_to_rec |
steps/qc_to_rec.cwl
(CommandLineTool)
|
||
| variantcall |
wf-variantcall.cwl
(Workflow)
|
||
| prep_samples |
steps/prep_samples.cwl
(CommandLineTool)
|
||
| summarize_vc |
steps/summarize_vc.cwl
(CommandLineTool)
|
||
| combine_calls |
steps/combine_calls.cwl
(CommandLineTool)
|
||
| alignment_to_rec |
steps/alignment_to_rec.cwl
(CommandLineTool)
|
||
| pipeline_summary |
steps/pipeline_summary.cwl
(CommandLineTool)
|
||
| batch_for_ensemble |
steps/batch_for_ensemble.cwl
(CommandLineTool)
|
||
| prep_samples_to_rec |
steps/prep_samples_to_rec.cwl
(CommandLineTool)
|
||
| batch_for_variantcall |
steps/batch_for_variantcall.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 |
|---|---|---|---|
| umi_bam | File[] | ||
| align_bam | File[] | ||
| variants__gvcf | 9f206e30fa81b4c659506d07b6e10a29[] | ||
| variants__calls | aef93e3c88224c2ed9426e4c0bec7e7b[] | ||
| rgnames__sample_out | String[] | ||
| regions__sample_callable | File[] | ||
| validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/7c46d5c6ef6501dc0e07a9b740e9de64ffec83f5/somatic/somatic-workflow/main-somatic.cwl
