Workflow: main-giab-chm.cwl
Fetched 2024-04-19 13:36:12 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 | af0b0fecb1082637840b185a1daf97d2[] | ||
| 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 | 38762c712568b26856817382cf361c9c[] | ||
| reference__fasta__base | File[] | ||
| reference__genome_context | d93c996026d2569ddb754c7fbd444cdb[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__adapters | 4a496df74980d66e30d0bb6cd1e4af6a[] | ||
| config__algorithm__coverage | File[] | ||
| config__algorithm__tools_on | ce7cfc9630fd7d7a184efbb9f45720bb[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__bam_clean | Boolean[] | ||
| config__algorithm__tools_off | 5190dae2c3d53695cb9b4154e392636f[] | ||
| reference__minimap2__indexes | 8132b241e7a85e16fc06fb2ed1899106[] | ||
| reference__snpeff__GRCh38_86 | File[] | ||
| config__algorithm__trim_reads | Boolean[] | ||
| config__algorithm__recalibrate | Boolean[] | ||
| config__algorithm__variantcaller | 236c562bc9b945d8723539ac880f1a7f[] | ||
| genome_resources__aliases__human | Boolean[] | ||
| genome_resources__variation__lcr | File[] | ||
| genome_resources__aliases__snpeff | String[] | ||
| config__algorithm__exclude_regions | 40a8a30997386959c2fe232452c849b7[] | ||
| 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 | 7a6e2b38c36baae66fa900171bf4794d[] | ||
| variants__calls | 1fbd8dc5c821eab03ba9000db02d9792[] | ||
| summary__multiqc | File[] | ||
| regions__sample_callable | File[] | ||
| validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/af9a5621efcb44c249697d6df071fe4defe389ac/giab-chm/giab-chm-workflow/main-giab-chm.cwl
