Workflow for Illumina Quality Control and Filtering Version 1
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Multiple paired datasets will be merged into single paired dataset.
Summary:
- FastQC on raw data files
- fastp for read quality trimming
- BBduk for phiX and (optional) rRNA filtering
- Kraken2 for taxonomic classification of reads (optional)
- BBmap for (contamination) filtering using given references (optional)
- FastQC on filtered (merged) data
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
How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| identifier | identifier used | Identifier for this dataset used in this workflow |
|
| threads | Number of threads | Number of threads to use for computational processes |
|
| memory | Maximum memory in MB | Maximum memory usage in MegaBytes |
|
| forward_reads | Forward reads | Forward sequence fastq file(s) locally |
|
| reverse_reads | Reverse reads | Reverse sequence fastq file(s) locally |
|
| skip_qc_unfiltered | Skip QC unfiltered | Skip FastQC analyses of raw input reads (default false) |
|
| skip_qc_filtered | Skip QC filtered | Skip FastQC analyses of filtered input reads (default false) |
|
| filter_rrna | filter rRNA | Optionally remove rRNA sequences from the reads (default false) |
|
| filter_references | Filter reference file(s) | References fasta file(s) for filtering |
|
| deduplicate | Deduplicate reads | Remove exact duplicate reads with fastp |
|
| kraken2_confidence | Kraken2 confidence threshold | Confidence score threshold (default 0.0) must be between [0, 1] |
|
| kraken2_database | Kraken2 database | Kraken2 database location, multiple databases is possible |
|
| kraken2_standard_report | Kraken2 standard report | Also output Kraken2 standard report with per read classification. These can be large. (default false) |
|
| keep_reference_mapped_reads | Keep mapped reads | Keep with reads mapped to the given reference (default false) |
|
| prepare_reference | Prepare references | Prepare references to a single fasta file and unique headers (default true). When false a single fasta file as reference is expected with unique headers |
|
| step | Output Step number | Step number for output folder numbering (default 1) |
|
| destination | Output Destination | Optional output destination only used for cwl-prov reporting. |
|
Steps
| ID | Name | Description |
|---|---|---|
| fastqc_illumina_before | FastQC before | Quality assessment and report of reads |
| fastq_merge_fwd | Merge forward reads | Merge multiple forward fastq reads to a single file |
| fastq_merge_rev | Merge reverse reads | Merge multiple reverse fastq reads to a single file |
| fastq_fwd_array_to_file | Fwd reads array to file | Forward file of single file array to file object |
| fastq_rev_array_to_file | Rev reads array to file | Forward file of single file array to file object |
| fastp | fastp | Read quality filtering and (barcode) trimming. |
| rrna_filter | rRNA filter (bbduk) | Filters rRNA sequences from reads using bbduk |
| reference_array_to_file | Reference array to file | Array to file object when the reference does not need to be prepared |
| prepare_fasta_db | Prepare references | Prepare references to a single fasta file and unique headers |
| reference_filter_illumina | Reference read mapping | Map reads against references using BBMap |
| phix_filter | PhiX filter (bbduk) | Filters illumina spike-in PhiX sequences from reads using bbduk |
| illumina_kraken2_unfiltered | Kraken2 unfiltered | Taxonomic classification on unfiltered files |
| illumina_kraken2_filtered | Kraken2 unfiltered | Taxonomic classification on unfiltered files |
| illumina_kraken2_compress | Compress kraken2 | Compress large kraken2 report file |
| illumina_kraken2_krona | Krona Kraken2 | Visualization of kraken2 with Krona |
| fastqc_illumina_after | FastQC after | Quality assessment and report of reads |
| reports_files_to_folder | Reports to folder | Preparation of fastp output files to a specific output folder |
| kraken2_files_to_folder | Kraken2 folder | Kraken2 files to single folder |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| reports_folder | Filtering reports folder | Folder containing all reports of filtering and quality control |
|
| kraken2_folder | Kraken2 folder | Folder with Kraken2 output files |
|
| QC_forward_reads | Filtered forward read | Filtered forward read |
|
| QC_reverse_reads | Filtered reverse read | Filtered reverse read |
|
Version History
Version 1 (earliest) Created 21st Apr 2022 at 14:00 by Bart Nijsse
Initial commit
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master5c2e0e5
Creators and Submitter
Views: 1511
Created: 21st Apr 2022 at 14:00
Last updated: 7th Apr 2023 at 15:02
AttributionsNone
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