Workflow: pipeline-bam2vcf-distr.cwl

Fetched 2022-01-20 11:57:59 GMT

DNAseq pipeline from bam to vcf in distributed mode

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Inputs

ID Type Title Doc
dedup_metrics_output_file String
threads Integer (Optional)
output_file String
dedup_output_bam String
reference File
realign_output_bam String
realign_known_sites File[]
qcal_output_file String
dbsnp File (Optional)
input_bam File[]
interval File (Optional)
bqsr_known_sites File[]
shard String[]

Steps

ID Runs Label Doc
bqsr

Run BQSR pre+post+plot flow with distribution

hc
realign
dedup

run 2-pass dedup: algo LocusCollector + algo Dedup sequentially in distributed mode

Outputs

ID Type Label Doc
output File
qcal_output File
qcal_plot_output File (Optional)
realign_output File
dedup_metric_output File (Optional)
dedup_output File
Permalink: https://w3id.org/cwl/view/git/d20382adfe7285cb517a25d95d2bcb7586546e23/pipeline/pipeline-bam2vcf-distr.cwl