Workflow: bam_readcount workflow

Fetched 2021-01-31 11:19:29 GMT
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Inputs

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

Steps

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

Outputs

ID Type Label Doc
normalized_vcf File
snv_bam_readcount_tsv File
indel_bam_readcount_tsv File
Permalink: https://w3id.org/cwl/view/git/3a287b7cb6162cdea79865235d224fea45963d87/definitions/subworkflows/bam_readcount.cwl