Workflow: main-NA12878-platinum-chr20.cwl
Fetched 2023-01-11 23:50:06 GMT
Verified with cwltool version 3.1.20221201130942
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- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| files | db8ae346c64446e133da0fe3203a135a[] | ||
| 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 | a34ec3ef009bbd528e07ec07e09d02ee[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| reference__genome_context | e411850250d3c6842a430a3f043402be[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__tools_on | a21efb409970b3cffa5803f4bc48333d[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__tools_off | 48aa1ff5aaac88d3d2ee7d1afc2afb2f[] | ||
| reference__snpeff__GRCh38_86 | File[] | ||
| config__algorithm__recalibrate | Boolean[] | ||
| config__algorithm__variantcaller | 98c5bd27c96e67d6a47c32a8adb63458[] | ||
| genome_resources__aliases__human | Boolean[] | ||
| genome_resources__aliases__snpeff | String[] | ||
| config__algorithm__mark_duplicates | Boolean[] | ||
| config__algorithm__variant_regions | String[] | ||
| 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)
|
||
| 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 | a329c97cc04b6dae696b963f36bcd20a[] | ||
| variants__calls | 656f23269692d795bc16da09b87e5685[] | ||
| summary__multiqc | File[] | ||
| regions__sample_callable | File[] | ||
| validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/9606af30d5f047745a1cd7ec1a59d65508ed256e/NA12878-chr20/NA12878-platinum-chr20-workflow/main-NA12878-platinum-chr20.cwl
