Workflow: main-somatic.cwl
Fetched 2023-01-12 06:38:32 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 | 07e3e6c4869d66f758d0342abed14375[] | ||
| 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[] | ||
| metadata__phenotype | String[] | ||
| reference__versions | File[] | ||
| config__algorithm__qc | 18ba2c5ba88daea718c88c1b2b587781[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| reference__snpeff__hg19 | File[] | ||
| reference__genome_context | 9dc88213abc58914611551457292309d[] | ||
| config__algorithm__aligner | Boolean[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__vcfanno | 48bb21802e1d872384b4f3882ee07314[] | ||
| config__algorithm__adapters | 39bfdf12612ceb643715206b15ef5191[] | ||
| config__algorithm__coverage | File[] | ||
| config__algorithm__ensemble | String[] | ||
| config__algorithm__tools_on | 10f452450226027b497ec7d24877a2a4[] | ||
| config__algorithm__umi_type | String[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__bam_clean | Boolean[] | ||
| config__algorithm__tools_off | 53789da30899927ee5945881248ebecf[] | ||
| reference__minimap2__indexes | 60fba30b2d4845f4dd8fb2aa46616d18[] | ||
| config__algorithm__trim_reads | Boolean[] | ||
| config__algorithm__recalibrate | Boolean[] | ||
| config__algorithm__variantcaller | 25701fa759b62e6304fd841591546c6a[] | ||
| 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 | b84388d8eed8f86e1de27b6dd2d92862[] | ||
| 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__gnomad_exome | File[] | ||
| 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)
|
||
| multiqc_summary |
steps/multiqc_summary.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 | 45153a52de3f12545e0bb2ecc7605035[] | ||
| versions__data | File[] | ||
| variants__calls | 6ca64bfad4a2b998dbd83af49851bf11[] | ||
| versions__tools | File[] | ||
| summary__multiqc | File[] | ||
| rgnames__sample_out | String[] | ||
| regions__sample_callable | File[] | ||
| validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/29c90b75a78ffbd7975c3d39f8e64b137da7450c/somatic/somatic-workflow/main-somatic.cwl
