Workflow: fastq2fasta.cwl

Fetched 2022-01-20 13:08:42 GMT
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Inputs

ID Type Title Doc
metadata File (Optional)
fastq_reverse File (Optional)
threads Integer
ref_fasta File
fastq_forward File

Steps

ID Runs Label Doc
samtools-sort
samtools-sort.cwl (CommandLineTool)

samtools sort, sort given bam file

bwa-mem
bwa-mem.cwl (CommandLineTool)

string

samtools-view
samtools-view.cwl (CommandLineTool)

samtools view to convert sam format to bam format

bam2fasta
bam2fasta.cwl (Workflow)
bam2fasta

Outputs

ID Type Label Doc
out_fasta File
out_metadata File (Optional)
Permalink: https://w3id.org/cwl/view/git/24465ba219711f2828e633d25d9f183e0f0eaccd/cwl/fastq2fasta/fastq2fasta.cwl