Workflow: pipeline-fastq2vcf-multisample.cwl

Fetched 2020-11-29 04:58:40 GMT

DNAseq pipeline from fastq to vcf for multiple samples

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Inputs

ID Type Title Doc
chunk_size Integer (Optional)
threads Integer (Optional)
sample String[]
platform String (Optional)
mark_secondary Boolean (Optional)
reference String
library String[]
input_reads 3f414db3cfcc948c1f947b67d7251c05[]
realign_known_sites String[]
dbsnp String (Optional)
interval String (Optional)
readgroup String[]
bqsr_known_sites String[]

Steps

ID Runs Label Doc
pipeline

DNAseq pipeline from fastq to vcf

Outputs

ID Type Label Doc
output File[]
qcal_plot_output File[] (Optional)
qcal_output File[]
realign_output File[]
dedup_metric_output File[] (Optional)
dedup_output File[]
bwa_output File[]
Permalink: https://w3id.org/cwl/view/git/d20382adfe7285cb517a25d95d2bcb7586546e23/pipeline/pipeline-fastq2vcf-multisample.cwl