Workflow: main-somatic.cwl
Fetched 2026-10-05 19:24:29 GMT
Verified with cwltool version 3.1.20230201224320
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- Default Values
- Nested Workflows
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- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| files | 817de9f0f961401807f11b88ed2af200[] | ||
| 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 | 050d82218dca377fea149ad427bf3831[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| reference__snpeff__hg19 | File[] | ||
| reference__genome_context | 44e185d87cf4793a11a6e399cc1b5d3b[] | ||
| config__algorithm__aligner | Boolean[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__vcfanno | f5c015435c252735c8b7b22169d3feef[] | ||
| config__algorithm__adapters | e566f046eeef7e98193f2b900630c0b4[] | ||
| config__algorithm__coverage | File[] | ||
| config__algorithm__tools_on | 8075063bc88f3608fdc40fa61da7e45d[] | ||
| config__algorithm__umi_type | String[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__bam_clean | Boolean[] | ||
| config__algorithm__tools_off | efee74485d3543c1ebd34798001c7d02[] | ||
| reference__minimap2__indexes | 825e769cfd2484dd108d365d5418d86f[] | ||
| config__algorithm__trim_reads | Boolean[] | ||
| config__algorithm__recalibrate | Boolean[] | ||
| config__algorithm__variantcaller | d0cbb1cec8fc939b25cf885033fc7224[] | ||
| genome_resources__aliases__human | Boolean[] | ||
| genome_resources__variation__lcr | String[] | ||
| genome_resources__aliases__snpeff | String[] | ||
| config__algorithm__exclude_regions | 3643a1a62c4d3c28417b0a461f020eb5[] | ||
| config__algorithm__mark_duplicates | Boolean[] | ||
| config__algorithm__variant_regions | File[] | ||
| genome_resources__aliases__ensembl | String[] | ||
| genome_resources__rnaseq__gene_bed | 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[] | ||
| config__algorithm__min_allele_fraction | Long[] | ||
| 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)
|
||
| multiqc_summary |
steps/multiqc_summary.cwl
(CommandLineTool)
|
||
| alignment_to_rec |
steps/alignment_to_rec.cwl
(CommandLineTool)
|
||
| pipeline_summary |
steps/pipeline_summary.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 | 20dcf19a1eef9492a48d51fbf4631e27[] | ||
| variants__calls | 35d0f205d0a4585d8e86afe8720cefd2[] | ||
| summary__multiqc | File[] | ||
| rgnames__sample_out | String[] | ||
| regions__sample_callable | File[] | ||
| validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/2e6d9d2bd834d98eb6f36c93cd0a9ed5ee52597b/somatic/somatic-workflow/main-somatic.cwl
