- 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 | 052773d15739baf908fe677ac61d59df[] | ||
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 | cf40b444cc4b97bbebd38877a015bd58[] | ||
reference__fasta__base | File[] | ||
reference__bwa__indexes | File[] | ||
reference__genome_context | 0cbecfc4ea4c7cc3b40b0eb59cc4774a[] | ||
config__algorithm__aligner | String[] | ||
config__algorithm__tools_on | e22647ebeb8a5b81614167e9375f17cd[] | ||
config__algorithm__validate | File[] | ||
config__algorithm__tools_off | 07094d5d00c57679b41539b3f9744ad5[] | ||
reference__snpeff__GRCh38_86 | File[] | ||
config__algorithm__recalibrate | Boolean[] | ||
config__algorithm__variantcaller | 2bcd4f5160f0c482aab3a41f04effafe[] | ||
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 | 56291b6468a7b7d9cd42c7c2c0b13058[] | ||
variants__calls | ed0537d01cad74b3d9624cb75202dd4e[] | ||
summary__multiqc | File[] | ||
regions__sample_callable | File[] | ||
validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/afd674a6d64fb4e115c0b3fe95b7bb1b73ec69a9/NA12878-chr20/NA12878-platinum-chr20-workflow/main-NA12878-platinum-chr20.cwl