Workflow: main-prealign.cwl

Fetched 2023-01-12 05:24:10 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
files 1b5012781a3e1e2c8f17bdd2f47bbe32[]
analysis String[]
vrn_file File[]
resources String[]
description String[]
genome_build String[]
reference__rtg File[]
metadata__batch String[]
rgnames__sample String[]
reference__twobit File[]
metadata__phenotype String[]
config__algorithm__qc da340ce8486fae6093cb18fbd8a11fc2[]
reference__fasta__base File[]
reference__snpeff__hg19 File[]
reference__genome_context 6dc7f19efe018bcdfbdfb1845c0326a5[]
config__algorithm__effects String[]
config__algorithm__vcfanno 0b8b6e02ea4b16e1dccccf57e1bbee81[]
config__algorithm__coverage File[]
config__algorithm__ensemble String[]
config__algorithm__tools_on d5b028826cdcd1dec530d57b788c4e2c[]
config__algorithm__validate String[]
config__algorithm__tools_off 3d835593eb4dc6a505e24f3e41eeb136[]
config__algorithm__recalibrate Boolean[]
config__algorithm__variantcaller Boolean[]
genome_resources__aliases__human Boolean[]
genome_resources__variation__esp File[]
genome_resources__variation__lcr String[]
genome_resources__aliases__snpeff String[]
genome_resources__variation__exac File[]
config__algorithm__exclude_regions af58d2e581b0a5e82049c7646ef89db5[]
config__algorithm__variant_regions File[]
genome_resources__aliases__ensembl String[]
genome_resources__rnaseq__gene_bed File[]
genome_resources__variation__1000g File[]
genome_resources__variation__dbsnp File[]
genome_resources__variation__polyx String[]
config__algorithm__nomap_split_size Long[]
config__algorithm__validate_regions String[]
genome_resources__variation__cosmic File[]
config__algorithm__coverage_interval String[]
genome_resources__variation__clinvar File[]
config__algorithm__min_allele_fraction Long[]
config__algorithm__nomap_split_targets Long[]
genome_resources__variation__train_hapmap File[]
genome_resources__variation__train_indels File[]
genome_resources__variation__encode_blacklist String[]

Steps

ID Runs Label Doc
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)
organize_noalign
steps/organize_noalign.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 2488270d9a566d79e3ec197d530b6755[]
variants__calls d895f2c942baeb12cef287861d28d0b8[]
summary__multiqc File[]
rgnames__sample_out String[]
regions__sample_callable File[]
validate__grading_summary File[]
Permalink: https://w3id.org/cwl/view/git/8541da9674f17a2f44bd4cb042a3c8a2bbd22e5d/prealign/prealign-workflow/main-prealign.cwl