Workflow: main-NA12878-platinum-chr20.cwl

Fetched 2023-01-12 06:45:32 GMT
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Inputs

ID Type Title Doc
files 052773d15739baf908fe677ac61d59df[]
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 cf40b444cc4b97bbebd38877a015bd58[]
reference__fasta__base File[]
reference__bwa__indexes File[]
reference__genome_context 0cbecfc4ea4c7cc3b40b0eb59cc4774a[]
config__algorithm__aligner String[]
config__algorithm__tools_on e22647ebeb8a5b81614167e9375f17cd[]
config__algorithm__validate File[]
config__algorithm__tools_off 07094d5d00c57679b41539b3f9744ad5[]
reference__snpeff__GRCh38_86 File[]
config__algorithm__recalibrate Boolean[]
config__algorithm__variantcaller 2bcd4f5160f0c482aab3a41f04effafe[]
genome_resources__aliases__human Boolean[]
genome_resources__aliases__snpeff String[]
config__algorithm__mark_duplicates Boolean[]
config__algorithm__variant_regions String[]
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)
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 56291b6468a7b7d9cd42c7c2c0b13058[]
variants__calls ed0537d01cad74b3d9624cb75202dd4e[]
summary__multiqc File[]
regions__sample_callable File[]
validate__grading_summary File[]
Permalink: https://w3id.org/cwl/view/git/afd674a6d64fb4e115c0b3fe95b7bb1b73ec69a9/NA12878-chr20/NA12878-platinum-chr20-workflow/main-NA12878-platinum-chr20.cwl