Workflow: main-giab-chm.cwl
Fetched 2023-01-11 23:51:30 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| files | cb153640aece6ad9d04f8066a2cd6a6d[] | ||
| analysis | String[] | ||
| vrn_file | String[] | ||
| 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 | 690b59956dbcb75eebb9e025f25f2970[] | ||
| reference__fasta__base | File[] | ||
| reference__genome_context | a087527b5b905322025a76c84bcffa82[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__adapters | 9f2b417acd904c5bc3de614d0f4a3028[] | ||
| config__algorithm__coverage | File[] | ||
| config__algorithm__tools_on | ee712febbbc21e8af2d991302fdf9f49[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__bam_clean | Boolean[] | ||
| config__algorithm__tools_off | 72f2dd6f26d03b378e04c89a915c8fed[] | ||
| reference__minimap2__indexes | 28237d6193953e27ed17cf090ba1693b[] | ||
| reference__snpeff__GRCh38_86 | File[] | ||
| config__algorithm__trim_reads | Boolean[] | ||
| config__algorithm__recalibrate | Boolean[] | ||
| config__algorithm__variantcaller | 92df773c8c93f75b8df886ed478b5ab8[] | ||
| genome_resources__aliases__human | Boolean[] | ||
| genome_resources__variation__lcr | File[] | ||
| genome_resources__aliases__snpeff | String[] | ||
| config__algorithm__exclude_regions | 25f663016510b77e7071cef27efe9921[] | ||
| 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 | File[] | ||
| config__algorithm__align_split_size | Boolean[] | ||
| config__algorithm__nomap_split_size | Long[] | ||
| config__algorithm__validate_regions | File[] | ||
| genome_resources__variation__cosmic | String[] | ||
| config__algorithm__coverage_interval | String[] | ||
| config__algorithm__nomap_split_targets | Long[] | ||
| 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 |
|---|---|---|---|
| align_bam | File[] | ||
| variants__gvcf | b1afd1cfd478eb5720244e8a11532076[] | ||
| variants__calls | d0587c54c7af05b2acc4ad5e9fbf4fd7[] | ||
| summary__multiqc | File[] | ||
| regions__sample_callable | File[] | ||
| validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/9606af30d5f047745a1cd7ec1a59d65508ed256e/giab-chm/giab-chm-workflow/main-giab-chm.cwl
