Workflow: main-giab-joint.cwl
Fetched 2025-05-18 06:12:48 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 | 4ff92cedc2c5bde24c3d667daa1dd7ee[] | ||
| analysis | 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 | c4983d229cd44c7cdf5886a51a33019c[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| reference__genome_context | b9d314550b847157904d5d3028ad5dd4[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__coverage | File[] | ||
| config__algorithm__tools_on | f7cf0486f1e6965a4ce6180435e98c9b[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__tools_off | 9c2e69520a648cef8daab70770f9b7a8[] | ||
| reference__snpeff__GRCh38_86 | File[] | ||
| config__algorithm__recalibrate | Boolean[] | ||
| config__algorithm__variantcaller | ee840d3c4cf85542e07977bd3ee139d1[] | ||
| genome_resources__aliases__human | Boolean[] | ||
| genome_resources__aliases__snpeff | String[] | ||
| 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[] | ||
| config__algorithm__align_split_size | String[] | ||
| 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[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| alignment |
wf-alignment.cwl
(Workflow)
|
||
| jointcall |
wf-jointcall.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)
|
||
| batch_for_jointvc |
steps/batch_for_jointvc.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 | 92f7a2584487be8e8cd8b90e94ebbfc2[] | ||
| variants__calls | dc402de00cfefa4852c1efb8ae5df819[] | ||
| summary__multiqc | File[] | ||
| regions__sample_callable | File[] | ||
| validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/af9a5621efcb44c249697d6df071fe4defe389ac/giab-joint/giab-joint-workflow/main-giab-joint.cwl
