Workflow: main-NA24385-sv.cwl

Fetched 2020-08-14 16:06:46 GMT
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Inputs

ID Type Title Doc
config__algorithm__svcaller f4f5127b1a8ef7e4107aac88e368528f[]
config__algorithm__qc 665e3c1415d16ee9b8856aee3dcfe2ee[]
config__algorithm__exclude_regions 4c2d8dcdedb5e6afb5b08779c4b28145[]
config__algorithm__recalibrate Boolean[]
config__algorithm__coverage_interval https://w3id.org/cwl/salad#null[]
reference__twobit File[]
reference__fasta__base File[]
description String[]
genome_resources__variation__dbsnp File[]
genome_resources__variation__lcr File[]
genome_resources__variation__polyx File[]
reference__snpeff__GRCh37_75 File[]
genome_resources__rnaseq__gene_bed File[]
rgnames__sample String[]
config__algorithm__mark_duplicates Boolean[]
config__algorithm__nomap_split_targets Long[]
genome_resources__variation__encode_blacklist File[]
config__algorithm__trim_reads Boolean[]
metadata__phenotype String[]
config__algorithm__nomap_split_size Long[]
genome_resources__aliases__snpeff String[]
config__algorithm__aligner String[]
config__algorithm__tools_off 78db39b82c6cbc7ca085016266b4b5e1[]
rgnames__lane String[]
rgnames__pu String[]
resources String[]
config__algorithm__bam_clean Boolean[]
analysis String[]
rgnames__pl String[]
config__algorithm__adapters 6580f9788e55a20acde5ed9c26041dcc[]
config__algorithm__align_split_size Boolean[]
metadata__batch https://w3id.org/cwl/salad#null[]
reference__minimap2__indexes d3d0af901edf92d77c4eb28ba40814e0[]
config__algorithm__variant_regions File[]
rgnames__lb https://w3id.org/cwl/salad#null[]
config__algorithm__coverage File[]
rgnames__rg String[]
files 2ae83a9cff4d846202c3ff120790b8f9[]
config__algorithm__tools_on 16192a59c940c72fa48fe2efa9c46ae7[]
genome_build String[]
config__algorithm__svvalidate File[]

Steps

ID Runs Label Doc
calculate_sv_bins
steps/calculate_sv_bins.cwl (CommandLineTool)
pipeline_summary
steps/pipeline_summary.cwl (CommandLineTool)
prep_samples
steps/prep_samples.cwl (CommandLineTool)
summarize_sv
steps/summarize_sv.cwl (CommandLineTool)
multiqc_summary
steps/multiqc_summary.cwl (CommandLineTool)
alignment_to_rec
steps/alignment_to_rec.cwl (CommandLineTool)
normalize_sv_coverage
steps/normalize_sv_coverage.cwl (CommandLineTool)
svcall
wf-svcall.cwl (Workflow)
qc_to_rec
steps/qc_to_rec.cwl (CommandLineTool)
batch_for_sv
steps/batch_for_sv.cwl (CommandLineTool)
postprocess_alignment_to_rec
steps/postprocess_alignment_to_rec.cwl (CommandLineTool)
postprocess_alignment
steps/postprocess_alignment.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)
calculate_sv_coverage
steps/calculate_sv_coverage.cwl (CommandLineTool)

Outputs

ID Type Label Doc
svvalidate__grading_summary https://w3id.org/cwl/salad#null[]
sv__calls 91e8cae1ce4cf9eb054a74a9be16cee1[]
rgnames__sample_out String[]
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/a297e87e014de998b8df9c90700c29173ec09932/NA24385-sv/NA24385-sv-workflow/main-NA24385-sv.cwl