Workflow: bam_readcount workflow

Fetched 2022-01-20 02:58:04 GMT
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Inputs

ID Type Title Doc
min_base_quality Integer (Optional)
min_mapping_quality Integer (Optional)
vcf File
reference_fasta File
sample String
bam File

Steps

ID Runs Label Doc
normalize_variants
../tools/normalize_variants.cwl (CommandLineTool)
Normalize variants
bam_readcount
../tools/bam_readcount.cwl (CommandLineTool)
run bam-readcount
decompose_variants
../tools/vt_decompose.cwl (CommandLineTool)
run vt decompose

Outputs

ID Type Label Doc
normalized_vcf File
indel_bam_readcount_tsv File
snv_bam_readcount_tsv File
Permalink: https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/bam_readcount.cwl