Workflow: main-wes_chr21_test.cwl

Fetched 2024-07-19 11:43:32 GMT
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Inputs

ID Type Title Doc
files c1d62d0c7b1440247b3c9baf6790c4e3[]
analysis String[]
vrn_file 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[]
reference__versions File[]
config__algorithm__qc f032533a241a41185e4da061459d4c40[]
reference__fasta__base File[]
reference__bwa__indexes File[]
reference__genome_context 73d675062e40b3c8aa640ad78a23226a[]
config__algorithm__aligner String[]
config__algorithm__effects String[]
config__algorithm__vcfanno 1f26ec365a3288e7cd24f099acb71c73[]
config__algorithm__adapters b59fa60d6b544fa946fa425c813a004f[]
config__algorithm__ensemble String[]
config__algorithm__svcaller f6d78e51c52d3e36b56f762aedd32c7c[]
config__algorithm__tools_on 5d6bf24bd56c04143e6378244edab74c[]
config__algorithm__validate File[]
config__algorithm__bam_clean Boolean[]
config__algorithm__tools_off 40e33b3210db0ab157ddd88dc098f4b1[]
reference__snpeff__GRCh37_75 File[]
config__algorithm__svvalidate String[]
config__algorithm__trim_reads String[]
config__algorithm__recalibrate Boolean[]
config__algorithm__svprioritize String[]
config__algorithm__variantcaller 8f80e2e8b10cf265a9cb43ab830bf10b[]
genome_resources__aliases__human Boolean[]
genome_resources__variation__esp File[]
genome_resources__variation__lcr File[]
genome_resources__aliases__snpeff String[]
genome_resources__variation__exac File[]
config__algorithm__exclude_regions 107eb1eac3a97dedd7e81dc4641e3054[]
config__algorithm__mark_duplicates Boolean[]
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 File[]
config__algorithm__align_split_size String[]
config__algorithm__nomap_split_size Long[]
config__algorithm__validate_regions File[]
genome_resources__variation__cosmic File[]
config__algorithm__coverage_interval String[]
genome_resources__variation__clinvar File[]
config__algorithm__min_allele_fraction Double[]
config__algorithm__nomap_split_targets Long[]
genome_resources__variation__train_hapmap File[]
genome_resources__variation__train_indels File[]
genome_resources__variation__encode_blacklist File[]

Steps

ID Runs Label Doc
svcall
wf-svcall.cwl (Workflow)
alignment
wf-alignment.cwl (Workflow)
qc_to_rec
steps/qc_to_rec.cwl (CommandLineTool)
variantcall
wf-variantcall.cwl (Workflow)
batch_for_sv
steps/batch_for_sv.cwl (CommandLineTool)
prep_samples
steps/prep_samples.cwl (CommandLineTool)
summarize_sv
steps/summarize_sv.cwl (CommandLineTool)
summarize_vc
steps/summarize_vc.cwl (CommandLineTool)
combine_calls
steps/combine_calls.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)
calculate_sv_bins
steps/calculate_sv_bins.cwl (CommandLineTool)
batch_for_ensemble
steps/batch_for_ensemble.cwl (CommandLineTool)
prep_samples_to_rec
steps/prep_samples_to_rec.cwl (CommandLineTool)
batch_for_variantcall
steps/batch_for_variantcall.cwl (CommandLineTool)
calculate_sv_coverage
steps/calculate_sv_coverage.cwl (CommandLineTool)
normalize_sv_coverage
steps/normalize_sv_coverage.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[]
sv__calls f59b245d088895c45b7ee628f83a12d9[]
variants__gvcf cb5297b42c974e7264a40432604935fb[]
versions__data File[]
variants__calls c69b9c86f486e7708580594f9206fa38[]
versions__tools File[]
summary__multiqc File[]
sv__supplemental f300cb3dd6c0693cf5242c1dc5db56fe[]
rgnames__sample_out String[]
sv__prioritize__raw c0b40599c8c161afa4a1f6ad58192966[]
sv__prioritize__tsv 364c7093ef6383f4e5e33ee34f05a051[]
regions__sample_callable File[]
validate__grading_summary File
svvalidate__grading_summary File[]
Permalink: https://w3id.org/cwl/view/git/595f6f0a59b937a862f79378fbb19ef1653dca90/wes-agha-test/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl