Workflow: main-SGDP-recall.cwl

Fetched 2025-04-24 22:30:30 GMT
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Inputs

ID Type Title Doc
files 78c3256ba304f1ebcc4f15e7f7e008f8[]
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 173ed01d472dd9611cca900e82a03535[]
metadata__phenotype String[]
config__algorithm__qc f38cea62fd1f41496a4e6d1d0b923eb5[]
reference__fasta__base File[]
reference__bwa__indexes File[]
genome_resources__version Long[]
reference__genome_context 59c2871b41d88cc56682398cb0016ae2[]
config__algorithm__aligner String[]
config__algorithm__archive 8c7e2fa118fa7e68cc741eac9bb52c06[]
config__algorithm__effects String[]
config__algorithm__realign String[]
config__algorithm__svcaller b21a2ba86f2c9c5db341ed2630ed5766[]
config__algorithm__tools_on b2753a93ac46152c3f648839ad3bdd16[]
config__algorithm__validate https://w3id.org/cwl/salad#null[]
config__algorithm__tools_off 4ee189c7dbfe39bd5c79aef72942f491[]
config__algorithm__recalibrate String[]
config__algorithm__variantcaller 3442e1359f5832fdd1e6b6fb5e2c2102[]
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/9606af30d5f047745a1cd7ec1a59d65508ed256e/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl