Workflow: main-somatic.cwl

Fetched 2023-01-12 06:38:32 GMT
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Inputs

ID Type Title Doc
files 07e3e6c4869d66f758d0342abed14375[]
analysis String[]
vrn_file File[]
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[]
metadata__phenotype String[]
reference__versions File[]
config__algorithm__qc 18ba2c5ba88daea718c88c1b2b587781[]
reference__fasta__base File[]
reference__bwa__indexes File[]
reference__snpeff__hg19 File[]
reference__genome_context 9dc88213abc58914611551457292309d[]
config__algorithm__aligner Boolean[]
config__algorithm__effects String[]
config__algorithm__vcfanno 48bb21802e1d872384b4f3882ee07314[]
config__algorithm__adapters 39bfdf12612ceb643715206b15ef5191[]
config__algorithm__coverage File[]
config__algorithm__ensemble String[]
config__algorithm__tools_on 10f452450226027b497ec7d24877a2a4[]
config__algorithm__umi_type String[]
config__algorithm__validate File[]
config__algorithm__bam_clean Boolean[]
config__algorithm__tools_off 53789da30899927ee5945881248ebecf[]
reference__minimap2__indexes 60fba30b2d4845f4dd8fb2aa46616d18[]
config__algorithm__trim_reads Boolean[]
config__algorithm__recalibrate Boolean[]
config__algorithm__variantcaller 25701fa759b62e6304fd841591546c6a[]
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 b84388d8eed8f86e1de27b6dd2d92862[]
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 String[]
config__algorithm__align_split_size Long[]
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__gnomad_exome File[]
genome_resources__variation__train_hapmap File[]
genome_resources__variation__train_indels File[]
genome_resources__variation__encode_blacklist 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)
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)
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)
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
umi_bam File[]
align_bam File[]
variants__gvcf 45153a52de3f12545e0bb2ecc7605035[]
versions__data File[]
variants__calls 6ca64bfad4a2b998dbd83af49851bf11[]
versions__tools File[]
summary__multiqc File[]
rgnames__sample_out String[]
regions__sample_callable File[]
validate__grading_summary File[]
Permalink: https://w3id.org/cwl/view/git/29c90b75a78ffbd7975c3d39f8e64b137da7450c/somatic/somatic-workflow/main-somatic.cwl