Workflow: main-giab-chm.cwl

Fetched 2018-12-15 11:04:19 GMT
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Inputs

ID Type Title Doc
config__algorithm__qc 9592573f79a660ab94053d435d4254d0[]
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[]
config__algorithm__trim_reads Boolean[]
genome_resources__variation__encode_blacklist https://w3id.org/cwl/salad#null[]
metadata__phenotype String[]
genome_resources__aliases__human Boolean[]
vrn_file https://w3id.org/cwl/salad#null[]
config__algorithm__effects String[]
config__algorithm__tools_off e0c3de9456cc25966eb97318894122d3[]
config__algorithm__bam_clean Boolean[]
analysis String[]
reference__rtg File[]
config__algorithm__adapters f7fb2167ef56f54f9d110def93eab3d9[]
config__algorithm__variant_regions File[]
config__algorithm__validate_regions File[]
rgnames__rg String[]
config__algorithm__tools_on 20dddcb340e4bac42aebfa051bf0325b[]
files 773ebe70267190d7895f574961e8ccbc[]
config__algorithm__exclude_regions 3971b538b6cc9961db39bf082f09b4aa[]
description String[]
genome_resources__variation__lcr File[]
genome_resources__variation__polyx File[]
genome_resources__rnaseq__gene_bed File[]
rgnames__sample String[]
reference__genome_context 94aaf53d7f7124a9c15a795e0bb2a332[]
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[]
metadata__batch https://w3id.org/cwl/salad#null[]
config__algorithm__align_split_size Boolean[]
reference__minimap2__indexes ec391c3a0665a4318fce205fde25b05a[]
genome_resources__aliases__ensembl String[]
rgnames__lb https://w3id.org/cwl/salad#null[]
config__algorithm__coverage File[]
genome_build String[]
config__algorithm__variantcaller 46e7cb4e34b9cc62456eb9492299391e[]

Steps

ID Runs Label Doc
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)
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 0d0cdd25d9263d5d6284b21f77d665e9[]
validate__grading_summary https://w3id.org/cwl/salad#null[]
variants__calls 90a32d182593b03d08590fa961ae76c8[]
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/afd674a6d64fb4e115c0b3fe95b7bb1b73ec69a9/giab-chm/giab-chm-workflow/main-giab-chm.cwl