Workflow: bam_readcount workflow

Fetched 2023-01-09 22:53:15 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs sample sample bam_readcount run bam-readcount sample->bam_readcount sample vcf vcf normalize_variants Normalize variants vcf->normalize_variants vcf min_base_quality min_base_quality min_base_quality->bam_readcount min_base_quality min_mapping_quality min_mapping_quality min_mapping_quality->bam_readcount min_mapping_quality bam bam bam->bam_readcount bam reference_fasta reference_fasta reference_fasta->bam_readcount reference_fasta reference_fasta->normalize_variants reference normalized_vcf normalized_vcf indel_bam_readcount_tsv indel_bam_readcount_tsv snv_bam_readcount_tsv snv_bam_readcount_tsv bam_readcount->indel_bam_readcount_tsv bam_readcount->snv_bam_readcount_tsv decompose_variants run vt decompose normalize_variants->decompose_variants vcf decompose_variants->normalized_vcf decompose_variants->bam_readcount vcf
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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/061d3a2fbcd8a1c39c0b38c549e528deb24a9d54/definitions/subworkflows/bam_readcount.cwl