Workflow: main-giab-joint.cwl

Fetched 2019-01-11 18:37:50 GMT
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Inputs

ID Type Title Doc
config__algorithm__qc 9582fe1b6d0bb59910996e833c7a88cf[]
config__algorithm__recalibrate Boolean[]
reference__twobit File[]
config__algorithm__coverage_interval https://w3id.org/cwl/salad#null[]
reference__fasta__base File[]
description String[]
genome_resources__variation__cosmic https://w3id.org/cwl/salad#null[]
genome_resources__variation__dbsnp File[]
reference__snpeff__GRCh38_86 File[]
genome_resources__rnaseq__gene_bed File[]
config__algorithm__mark_duplicates Boolean[]
rgnames__sample String[]
config__algorithm__nomap_split_targets Long[]
reference__genome_context 4164f8cae7fad30a5d84899e2e80eea5[]
metadata__phenotype String[]
genome_resources__aliases__human Boolean[]
config__algorithm__nomap_split_size Long[]
genome_resources__aliases__snpeff String[]
config__algorithm__aligner String[]
rgnames__lane String[]
config__algorithm__tools_off 2f91d017e49441f4b4b2ed5aacae8f1a[]
rgnames__pu String[]
config__algorithm__validate File[]
resources String[]
analysis String[]
reference__rtg File[]
rgnames__pl String[]
metadata__batch String[]
config__algorithm__align_split_size https://w3id.org/cwl/salad#null[]
config__algorithm__variant_regions File[]
config__algorithm__coverage File[]
rgnames__lb https://w3id.org/cwl/salad#null[]
config__algorithm__validate_regions File[]
genome_resources__aliases__ensembl String[]
rgnames__rg String[]
config__algorithm__tools_on 6dc6ac42e18f35429bb885b97f9a1cb1[]
files c3bd346387edd675175f67171838e342[]
genome_build String[]
reference__bwa__indexes File[]
config__algorithm__variantcaller 0910f03d2a152deda99147cc91626e6b[]

Steps

ID Runs Label Doc
batch_for_jointvc
steps/batch_for_jointvc.cwl (CommandLineTool)
jointcall
wf-jointcall.cwl (Workflow)
pipeline_summary
steps/pipeline_summary.cwl (CommandLineTool)
multiqc_summary
steps/multiqc_summary.cwl (CommandLineTool)
prep_samples
steps/prep_samples.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)
postprocess_alignment
steps/postprocess_alignment.cwl (CommandLineTool)
variantcall
wf-variantcall.cwl (Workflow)
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 fb072c2e4bea8ee1d9600faa0412957c[]
validate__grading_summary https://w3id.org/cwl/salad#null[]
variants__calls bafbcbfca5628422854189d1ee945895[]
summary__multiqc https://w3id.org/cwl/salad#null[]
regions__sample_callable File[]
align_bam File[]
Permalink: https://w3id.org/cwl/view/git/afd674a6d64fb4e115c0b3fe95b7bb1b73ec69a9/giab-joint/giab-joint-workflow/main-giab-joint.cwl