Workflow: Nanopore Quality Control and Filtering

Fetched 2024-04-26 23:25:05 GMT

**Workflow for nanopore read quality control and contamination filtering.** - FastQC before filtering (read quality control) - Kraken2 taxonomic read classification - Minimap2 read filtering based on given references - FastQC after filtering (read quality control) **All tool CWL files and other workflows can be found here:**<br> Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl<br> Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows<br> WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

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Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
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  • Inputs/Outputs

Inputs

ID Type Title Doc
step Integer (Optional) CWL base step number

Step number for order of steps
reads String[] Forward reads

Forward sequence file locally
memory Integer (Optional) Maximum memory in MB

Maximum memory usage in megabytes
threads Integer (Optional) Number of threads

Number of threads to use for computational processes
identifier String identifier used

Identifier for this dataset used in this workflow
destination String (Optional) Output Destination

Optional Output destination used for cwl-prov reporting.
run_kraken2 Boolean (Optional) Kraken2

Optionally run kraken2 contamination inspection
kraken_database String (Optional) Kraken2 database

Kraken2 database location
filter_references String[] Contamination reference file

Contamination references fasta file for contamination filtering
keep_reference_mapped_reads Boolean Keep mapped reads

Keep with reads mapped to the given reference

Steps

ID Runs Label Doc
workflow_krona
../krona/krona.cwl (CommandLineTool)
Krona

Visualization of Kraken2 report results. ktImportText -o $1 $2

combine_references
../bash/concatenate.cwl (CommandLineTool)
Concatenate multiple files
merge_nanopore_fastq
../bash/concatenate.cwl (CommandLineTool)
Concatenate multiple files
fastqc_nanopore_after
../fastqc/fastqc.cwl (CommandLineTool)
FASTQC

Performs quality control on FASTQ files

fastqc_nanopore_before
../fastqc/fastqc.cwl (CommandLineTool)
FASTQC

Performs quality control on FASTQ files

reports_files_to_folder
../expressions/files_to_folder.cwl (ExpressionTool)

Transforms the input files to a mentioned directory

reference_filter_nanopore
../minimap2/minimap2_to_fastq.cwl (CommandLineTool)
Minimap2 to (un)mapped long reads

Get unmapped or mapped long reads reads in fastq.gz format using minimap2 and samtools. Mainly used for contamination removal. - requires pigz! minimap2 | samtools | pigz

workflow_nanopore_kraken2
../kraken2/kraken2.cwl (CommandLineTool)
Kraken2 metagenomics read classification

Kraken2 metagenomics read classification.

Updated databases available at: https://benlangmead.github.io/aws-indexes/k2 (e.g. PlusPF-8) Original db: https://ccb.jhu.edu/software/kraken2/index.shtml?t=downloads

Outputs

ID Type Label Doc
filtered_reads File Filtered nanopore reads

Filtered nanopore reads
reports_folder Directory Filtering reports folder

Folder containing all reports of filtering and quality control
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/b9097b82e6ab6f2c9496013ce4dd6877092956a0/cwl/workflows/workflow_nanopore_quality.cwl