Workflow: main-giab-chm.cwl

Fetched 2023-01-12 06:56:20 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
files 68552eb8a2880eb6069b686fe204c56e[]
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 714518207be1abe873f2ef060ba7a1fe[]
reference__fasta__base File[]
reference__genome_context f9dd4f135bba664d6b18107ce9f1800f[]
config__algorithm__aligner String[]
config__algorithm__effects String[]
config__algorithm__adapters 6d7835b21a5faf74d96b56679864fe59[]
config__algorithm__coverage File[]
config__algorithm__tools_on a106bb625c4d9a227fc894c51952744d[]
config__algorithm__validate File[]
config__algorithm__bam_clean Boolean[]
config__algorithm__tools_off bbd5070d8f317459e7c2ef665cc02951[]
reference__minimap2__indexes 0648134d30170b17d967e028e55e145b[]
reference__snpeff__GRCh38_86 File[]
config__algorithm__trim_reads Boolean[]
config__algorithm__recalibrate Boolean[]
config__algorithm__variantcaller 969bb2b9357515a7effc023451b20cef[]
genome_resources__aliases__human Boolean[]
genome_resources__variation__lcr File[]
genome_resources__aliases__snpeff String[]
config__algorithm__exclude_regions 1397598c6466ba8601e158fb777f1806[]
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 String[]
config__algorithm__coverage_interval String[]
config__algorithm__nomap_split_targets Long[]
genome_resources__variation__encode_blacklist String[]

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 6e1736174e277b300084380baf28252e[]
variants__calls c94fef6a355efa1320afdc00aa28009e[]
summary__multiqc File[]
regions__sample_callable File[]
validate__grading_summary File[]
Permalink: https://w3id.org/cwl/view/git/afd674a6d64fb4e115c0b3fe95b7bb1b73ec69a9/giab-chm/giab-chm-workflow/main-giab-chm.cwl