Workflow: kfdrc_cram_to_gvcf.cwl

Fetched 2020-11-29 11:28:50 GMT
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Inputs

ID Type Title Doc
output_basename String
reference_dict File
biospecimen_name String
wgs_calling_interval_list File
dbsnp_vcf File
indexed_reference_fasta File
wgs_evaluation_interval_list File
contamination Float
input_cram File

Steps

ID Runs Label Doc
picard_renamesample
../tools/picard_renamesample.cwl (CommandLineTool)
gatk_haplotypecaller
../tools/gatk_haplotypecaller_cram.cwl (CommandLineTool)
picard_collectgvcfcallingmetrics
../tools/picard_collectgvcfcallingmetrics.cwl (CommandLineTool)
picard_mergevcfs
../tools/picard_mergevcfs.cwl (CommandLineTool)
picard_intervallisttools
../tools/picard_intervallisttools.cwl (CommandLineTool)

Outputs

ID Type Label Doc
gvcf_calling_metrics File[]
gvcf_renamed File
Permalink: https://w3id.org/cwl/view/git/c8255e2aab840f671d9f142d74f915c76415ff51/workflows/kfdrc_cram_to_gvcf.cwl