Workflow: main-NA12878-platinum-chr20.cwl

Fetched 2023-01-12 07:37:40 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
files 6fabfbc1df7ad458c9e69903b5272572[]
analysis String[]
vrn_file https://w3id.org/cwl/salad#null[]
description String[]
rgnames__lb https://w3id.org/cwl/salad#null[]
rgnames__pl String[]
rgnames__pu String[]
rgnames__rg String[]
genome_build String[]
rgnames__lane String[]
reference__rtg File[]
metadata__batch https://w3id.org/cwl/salad#null[]
rgnames__sample String[]
reference__viral 767761426d02264c4d3ac99520a97268[]
reference__snpeff File[]
metadata__phenotype String[]
config__algorithm__qc aaabef6fe6056b0386b8fa42cc91b967[]
reference__fasta__base File[]
reference__bwa__indexes File[]
genome_resources__version Long[]
reference__genome_context 79cdd5ecc57e0e033f3cd4133aeda466[]
config__algorithm__aligner String[]
config__algorithm__archive 0b8c3d326b0ff22e500b1d51c6c5ed0f[]
config__algorithm__effects String[]
config__algorithm__realign String[]
config__algorithm__tools_on 8df9193b64fd0fd93929836e921ddcea[]
config__algorithm__validate File[]
config__algorithm__tools_off 64c53bec89a6bc1085c453626580340b[]
config__algorithm__recalibrate String[]
config__algorithm__variantcaller 999a67f0335b14077f7d42042fd7f778[]
genome_resources__aliases__human String[]
genome_resources__rnaseq__dexseq File[]
genome_resources__variation__lcr File[]
genome_resources__aliases__snpeff String[]
genome_resources__rnaseq__refflat File[]
config__algorithm__mark_duplicates String[]
config__algorithm__variant_regions https://w3id.org/cwl/salad#null[]
genome_resources__aliases__ensembl String[]
genome_resources__variation__dbsnp File[]
config__algorithm__align_split_size https://w3id.org/cwl/salad#null[]
config__algorithm__nomap_split_size Long[]
config__algorithm__validate_regions File[]
genome_resources__variation__cosmic https://w3id.org/cwl/salad#null[]
config__algorithm__coverage_interval https://w3id.org/cwl/salad#null[]
genome_resources__rnaseq__transcripts File[]
config__algorithm__nomap_split_targets Long[]
genome_resources__variation__sv_repeat File[]
genome_resources__variation__qsignature File[]
genome_resources__variation__train_omni File[]
genome_resources__variation__train_1000g File[]
genome_resources__variation__train_hapmap File[]
genome_resources__variation__train_indels File[]
genome_resources__rnaseq__transcripts_mask File[]
genome_resources__rnaseq__transcriptome_index__tophat 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)
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)
summarize_grading_vc
steps/summarize_grading_vc.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[]
summary__multiqc File[]
validate__grading_summary File[]
Permalink: https://w3id.org/cwl/view/git/6e9274ca22e75e3359b5ff74c6657f300138bb95/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/main-NA12878-platinum-chr20.cwl