Workflow: main-giab-chm.cwl

Fetched 2019-07-23 15:31:20 GMT
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Inputs

ID Type Title Doc
config__algorithm__qc 1cab46815e95b330bded1f87415f91ab[]
config__algorithm__recalibrate Boolean[]
reference__twobit File[]
config__algorithm__coverage_interval https://w3id.org/cwl/salad#null[]
reference__fasta__base File[]
genome_resources__variation__cosmic https://w3id.org/cwl/salad#null[]
genome_resources__variation__dbsnp File[]
reference__snpeff__GRCh38_86 File[]
config__algorithm__mark_duplicates Boolean[]
config__algorithm__nomap_split_targets Long[]
genome_resources__variation__encode_blacklist https://w3id.org/cwl/salad#null[]
config__algorithm__trim_reads Boolean[]
metadata__phenotype String[]
genome_resources__aliases__human Boolean[]
vrn_file https://w3id.org/cwl/salad#null[]
config__algorithm__effects String[]
config__algorithm__tools_off 4f04f6b437586e25b86c458dd8eb3cef[]
config__algorithm__bam_clean Boolean[]
analysis String[]
reference__rtg File[]
config__algorithm__adapters 2d4937f6d1f06bd8b3d4f186c9269930[]
config__algorithm__variant_regions File[]
config__algorithm__validate_regions File[]
rgnames__rg String[]
files a8ded09c5106127a29a764e601207d4c[]
config__algorithm__tools_on 6bb485c46b72bdc7de4062b1d7f1dc97[]
config__algorithm__exclude_regions 573539b45d1e258c6d8fb21ac9af54d6[]
description String[]
genome_resources__variation__lcr File[]
genome_resources__variation__polyx File[]
genome_resources__rnaseq__gene_bed File[]
rgnames__sample String[]
reference__genome_context c46e4f59fb2e791a5f634f3d04459759[]
config__algorithm__nomap_split_size Long[]
genome_resources__aliases__snpeff String[]
config__algorithm__aligner String[]
rgnames__lane String[]
config__algorithm__validate File[]
rgnames__pu String[]
resources String[]
rgnames__pl String[]
config__algorithm__align_split_size Boolean[]
metadata__batch https://w3id.org/cwl/salad#null[]
reference__minimap2__indexes c28490da9109c49d965f64402460f66e[]
rgnames__lb https://w3id.org/cwl/salad#null[]
config__algorithm__coverage File[]
genome_resources__aliases__ensembl String[]
genome_build String[]
config__algorithm__variantcaller 628ce6d743c54f2ab61bee209f7307a6[]

Steps

ID Runs Label Doc
pipeline_summary
steps/pipeline_summary.cwl (CommandLineTool)
prep_samples
steps/prep_samples.cwl (CommandLineTool)
multiqc_summary
steps/multiqc_summary.cwl (CommandLineTool)
alignment_to_rec
steps/alignment_to_rec.cwl (CommandLineTool)
summarize_vc
steps/summarize_vc.cwl (CommandLineTool)
qc_to_rec
steps/qc_to_rec.cwl (CommandLineTool)
postprocess_alignment_to_rec
steps/postprocess_alignment_to_rec.cwl (CommandLineTool)
variantcall
wf-variantcall.cwl (Workflow)
postprocess_alignment
steps/postprocess_alignment.cwl (CommandLineTool)
batch_for_variantcall
steps/batch_for_variantcall.cwl (CommandLineTool)
alignment
wf-alignment.cwl (Workflow)
combine_sample_regions
steps/combine_sample_regions.cwl (CommandLineTool)
prep_samples_to_rec
steps/prep_samples_to_rec.cwl (CommandLineTool)

Outputs

ID Type Label Doc
variants__gvcf 2a508f0a6fea3e943548a6e343af3ac3[]
validate__grading_summary https://w3id.org/cwl/salad#null[]
variants__calls 5cccecaed1c4f67cc47f7ff323660e2d[]
summary__multiqc https://w3id.org/cwl/salad#null[]
regions__sample_callable https://w3id.org/cwl/salad#null[]
align_bam https://w3id.org/cwl/salad#null[]
Permalink: https://w3id.org/cwl/view/git/a297e87e014de998b8df9c90700c29173ec09932/giab-chm/giab-chm-workflow/main-giab-chm.cwl