Workflow: bam to trimmed fastqs

Fetched 2022-01-20 14:42:24 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
adapters File
min_readlength Integer
adapter_min_overlap Integer
adapter_trim_end String
max_uncalled Integer
bam File

Steps

ID Runs Label Doc
trim_fastq
../tools/trim_fastq.cwl (CommandLineTool)
Trim FASTQ (flexbar)
bam_to_fastq
../tools/bam_to_fastq.cwl (CommandLineTool)
Picard: BAM to FASTQ

Outputs

ID Type Label Doc
fastqs File[]
fastq2 File
fastq1 File
Permalink: https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/bam_to_trimmed_fastq.cwl