Workflow: main-SGDP-recall.cwl

Fetched 2023-01-12 06:14:54 GMT
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Inputs

ID Type Title Doc
files f4f13c1a3542862065efbcf049caf6cb[]
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[]
metadata__sex String[]
rgnames__lane String[]
reference__rtg File[]
metadata__batch https://w3id.org/cwl/salad#null[]
rgnames__sample String[]
reference__viral f78f285329f9cf4e229b96b45ae256a4[]
metadata__phenotype String[]
config__algorithm__qc e872dd3eaf1af7403ac19dbf4b71a213[]
reference__fasta__base File[]
reference__bwa__indexes File[]
genome_resources__version Long[]
reference__genome_context a8bc3f155d8907a396de96a13e239eb3[]
config__algorithm__aligner String[]
config__algorithm__archive 9bf4eee2fd1c9324aca172594048549a[]
config__algorithm__effects String[]
config__algorithm__realign String[]
config__algorithm__svcaller 2d2c85c2004438b66a0b13a74c408c72[]
config__algorithm__tools_on 59ea5fce27a622374a91257f1ab6cd8f[]
config__algorithm__validate https://w3id.org/cwl/salad#null[]
config__algorithm__tools_off 946ba826ab410b087bc00ba22dcb2f89[]
config__algorithm__recalibrate String[]
config__algorithm__variantcaller 7cec1b1b77b55e98be6bd90bfcd714a8[]
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 https://w3id.org/cwl/salad#null[]
genome_resources__variation__cosmic https://w3id.org/cwl/salad#null[]
config__algorithm__coverage_interval https://w3id.org/cwl/salad#null[]
config__algorithm__ensemble__numpass Long[]
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/afd674a6d64fb4e115c0b3fe95b7bb1b73ec69a9/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl