Workflow: main-giab-chm.cwl

Fetched 2024-04-23 04:12:45 GMT
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Inputs

ID Type Title Doc
files af0b0fecb1082637840b185a1daf97d2[]
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 38762c712568b26856817382cf361c9c[]
reference__fasta__base File[]
reference__genome_context d93c996026d2569ddb754c7fbd444cdb[]
config__algorithm__aligner String[]
config__algorithm__effects String[]
config__algorithm__adapters 4a496df74980d66e30d0bb6cd1e4af6a[]
config__algorithm__coverage File[]
config__algorithm__tools_on ce7cfc9630fd7d7a184efbb9f45720bb[]
config__algorithm__validate File[]
config__algorithm__bam_clean Boolean[]
config__algorithm__tools_off 5190dae2c3d53695cb9b4154e392636f[]
reference__minimap2__indexes 8132b241e7a85e16fc06fb2ed1899106[]
reference__snpeff__GRCh38_86 File[]
config__algorithm__trim_reads Boolean[]
config__algorithm__recalibrate Boolean[]
config__algorithm__variantcaller 236c562bc9b945d8723539ac880f1a7f[]
genome_resources__aliases__human Boolean[]
genome_resources__variation__lcr File[]
genome_resources__aliases__snpeff String[]
config__algorithm__exclude_regions 40a8a30997386959c2fe232452c849b7[]
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 7a6e2b38c36baae66fa900171bf4794d[]
variants__calls 1fbd8dc5c821eab03ba9000db02d9792[]
summary__multiqc File[]
regions__sample_callable File[]
validate__grading_summary File[]
Permalink: https://w3id.org/cwl/view/git/af9a5621efcb44c249697d6df071fe4defe389ac/giab-chm/giab-chm-workflow/main-giab-chm.cwl