Workflow: main-giab-joint.cwl

Fetched 2023-01-12 07:41:07 GMT
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Inputs

ID Type Title Doc
files 509f2da2c8dae3053cc80441273b54d2[]
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 b63e58415397e20b8f3485ac8fcdd3bf[]
reference__fasta__base File[]
reference__bwa__indexes File[]
reference__genome_context ff74382931a4393a27a6cddbcdc0875e[]
config__algorithm__aligner String[]
config__algorithm__coverage File[]
config__algorithm__tools_on 134360786d6f2abfeba9b718eadc869f[]
config__algorithm__validate File[]
config__algorithm__tools_off 1864214a625a1d1fce6d30073f59b94d[]
reference__snpeff__GRCh38_86 File[]
config__algorithm__recalibrate Boolean[]
config__algorithm__variantcaller ab8242066c6de8664ed22d4ed0b59df6[]
genome_resources__aliases__human Boolean[]
genome_resources__aliases__snpeff String[]
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[]
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)
jointcall
wf-jointcall.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)
batch_for_jointvc
steps/batch_for_jointvc.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 8ab1806e1fa50c8a785ce954149fd5f9[]
variants__calls 4f1c4bfca878394475c477f643c3e9dd[]
summary__multiqc File[]
regions__sample_callable File[]
validate__grading_summary File[]
Permalink: https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/giab-joint/giab-joint-workflow/main-giab-joint.cwl