Workflow: main-somatic-giab-mix.cwl
Fetched 2023-01-11 21:13:11 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 | 9013e3890f5b6fa6261e4d8a729e4645[] | ||
| 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 | c0a84e0fb3a8048a67c14afcad2cfad4[] | ||
| reference__fasta__base | File[] | ||
| reference__genome_context | 9532215dbf8d3d9585e839f686b9fb3a[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__adapters | e65f3e7cd2ad632b98591d5a38f3b034[] | ||
| config__algorithm__coverage | File[] | ||
| config__algorithm__tools_on | dc500dd919a68f9fb9c9e821ada856f7[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__bam_clean | Boolean[] | ||
| config__algorithm__tools_off | d062d2be55294970f400ab9f2463ea64[] | ||
| reference__minimap2__indexes | 6c22feae6c8f39dbd296795152b3624e[] | ||
| reference__snpeff__GRCh37_75 | File[] | ||
| config__algorithm__trim_reads | String[] | ||
| config__algorithm__recalibrate | Boolean[] | ||
| config__algorithm__variantcaller | a9861db33633f8840e6583de1fe4fdc6[] | ||
| genome_resources__aliases__human | Boolean[] | ||
| genome_resources__variation__lcr | File[] | ||
| genome_resources__aliases__snpeff | String[] | ||
| config__algorithm__exclude_regions | 90d392d1b7ed9cc9d110ab47ec9180f0[] | ||
| 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 | File[] | ||
| config__algorithm__coverage_interval | String[] | ||
| config__algorithm__nomap_split_targets | Long[] | ||
| genome_resources__variation__encode_blacklist | File[] |
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 | 195fde749789216e0ab3fed0883c2246[] | ||
| variants__calls | 16db300aa8bc229dfdd25eccdd1a313b[] | ||
| summary__multiqc | File[] | ||
| regions__sample_callable | File[] | ||
| validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/d7e640fb2359b4e81be071ad65af2730ad25d0bb/somatic-giab-mix/somatic-giab-mix-workflow/main-somatic-giab-mix.cwl
