Workflow: Preprocess fastq

Fetched 2023-01-05 03:12:28 GMT

Remove and trim low quality reads from fastq files. Return fasta files with reads passed and reads removed.

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Inputs

ID Type Title Doc
jobid String
maxLqb Integer
minQual Integer
minLength Integer
sequences File

Steps

ID Runs Label Doc
filter
../Tools/fastq-mcf.tool.cwl (CommandLineTool)
fastq-mcf

fastq quality trimmer >fastq-mcf 'n/a' <input> -S -k 0 -l <minLength> --max-ns <maxLqb> -q <minQual> -w <window> -o <outName>

adapterTrim
../Tools/autoskewer.tool.cwl (CommandLineTool)
autoskewer

detect and trim adapter sequences from reads >autoskewer.py -t <runtime.tmpdir> -i <input> -o <outName> -l <outLog>

passed2fasta
../Tools/seqUtil.tool.cwl (CommandLineTool)
seqUtil

Utility tool for various sequence file transformations.

removed2fasta
../Tools/seqUtil.tool.cwl (CommandLineTool)
seqUtil

Utility tool for various sequence file transformations.

Outputs

ID Type Label Doc
passed File
removed File
trimmed File
Permalink: https://w3id.org/cwl/view/git/6c5d0068bdb4f19a36a653c39964aefb9e5a7b1b/CWL/Workflows/preprocess-fastq.workflow.cwl