Workflow Type: Common Workflow Language
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Work-in-progress
Workflow for LongRead Quality Control and Filtering
- NanoPlot (read quality control) before and after filtering
- Filtlong (read trimming)
- Kraken2 taxonomic read classification before and after filtering
- Minimap2 read filtering based on given references
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
All tool CWL files and other workflows can be found here:
https://gitlab.com/m-unlock/cwl/workflows
How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html
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Inputs
ID | Name | Description | Type |
---|---|---|---|
identifier | identifier used | Identifier for this dataset used in this workflow |
|
nanopore_reads | Nanopore reads | Nanopore sequence file locally fastq format |
|
filter_references | Contamination reference file | Contamination references fasta file for contamination filtering |
|
keep_reference_mapped_reads | Keep mapped reads | Keep with reads mapped to the given reference |
|
kraken_database | Kraken2 database | Kraken2 database location, multiple databases is possible |
|
threads | Number of threads | Number of threads to use for computational processes |
|
memory | Maximum memory in MB | Maximum memory usage in megabytes |
|
step | CWL base step number | Step number for order of steps |
|
destination | Output Destination | Optional Output destination used for cwl-prov reporting. |
|
Steps
ID | Name | Description |
---|---|---|
merge_nanopore_fastq | Merge fastq files | n/a |
fastqc_nanopore_before | FastQC before | Quality assessment and report of reads before filter |
prepare_bbmap_db | Prepare references | Prepare BBMap references to a single fasta file and unique headers |
nanopore_array_to_file | array to file | Converts the file array to a single file object |
nanopore_quality_kraken2 | Kraken2 | Taxonomic classification of FASTQ reads |
nanopore_quality_kraken2_krona | Krona | Visualization of Kraken2 classification with Krona |
reference_filter_nanopore | Reference mapping | Removal of contaminated reads using minimap2 mapping |
fastqc_nanopore_after | FastQC after | Quality assessment and report of reads before filter |
reports_files_to_folder | Reports to folder | Preparation of fastp output files to a specific output folder |
Outputs
ID | Name | Description | Type |
---|---|---|---|
reports_folder | Filtering reports folder | Folder containing all reports of filtering and quality control |
|
filtered_reads | Filtered nanopore reads | Filtered nanopore reads |
|
Version History
Version 1 (earliest) Created 21st Apr 2022 at 17:19 by Bart Nijsse
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Views: 2230 Downloads: 249
Created: 21st Apr 2022 at 17:19
Last updated: 7th Apr 2023 at 15:07
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