Workflow: Illumina read quality control, trimming and contamination filter.
Fetched 2024-04-24 01:34:15 GMT
Verified with cwltool version 3.1.20221201130942
**Workflow for Illumina paired read quality control, trimming and filtering.**<br /> Multiple paired datasets will be merged into single paired dataset.<br /> Summary: - FastQC on raw data files<br /> - fastp for read quality trimming<br /> - BBduk for phiX and (optional) rRNA filtering<br /> - Kraken2 for taxonomic classification of reads (optional)<br /> - BBmap for (contamination) filtering using given references (optional)<br /> - FastQC on filtered (merged) data<br /> **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
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| step | Integer (Optional) | Output Step number |
Step number for output folder numbering |
| 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 |
| deduplicate | Boolean (Optional) | Deduplicate reads |
Remove exact duplicate reads with fastp |
| filter_rrna | Boolean | filter rRNA |
Optionally remove rRNA sequences from the reads. |
| forward_reads | String[] | Forward reads |
Forward sequence fastq file(s) locally |
| reverse_reads | String[] | Reverse reads |
Reverse sequence fastq file(s) locally |
| kraken_database | String[] (Optional) | Kraken2 database |
Kraken2 database location |
| filter_references | String[] (Optional) | Filter reference file(s) |
References fasta file(s) for filtering |
| keep_reference_mapped_reads | Boolean | Keep mapped reads |
Keep with reads mapped to the given reference |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastp |
../fastp/fastp.cwl
(CommandLineTool)
|
Modified from https://github.com/ambarishK/bio-cwl-tools/blob/release/fastp/fastp.cwl |
|
| phix_filter |
../bbmap/bbduk_filter.cwl
(CommandLineTool)
|
Filter from reads |
Filter reads using BBmaps bbduk tool (paired-end only) |
| rrna_filter |
../bbmap/bbduk_filter.cwl
(CommandLineTool)
|
Filter from reads |
Filter reads using BBmaps bbduk tool (paired-end only) |
| fastq_merge_fwd |
../bash/concatenate.cwl
(CommandLineTool)
|
Concatenate multiple files | |
| fastq_merge_rev |
../bash/concatenate.cwl
(CommandLineTool)
|
Concatenate multiple files | |
| combine_references |
../bash/concatenate.cwl
(CommandLineTool)
|
Concatenate multiple files | |
| fastqc_illumina_after |
../fastqc/fastqc.cwl
(CommandLineTool)
|
FASTQC |
Performs quality control on FASTQ files |
| fastqc_illumina_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 |
|
| illumina_quality_kraken2 |
../kraken2/kraken2.cwl
(CommandLineTool)
|
Kraken2 metagenomics read classification |
Kraken2 metagenomics read classification. |
| reference_filter_illumina |
../bbmap/bbmap_filter-reads.cwl
(CommandLineTool)
|
BBMap |
Read filtering using BBMap against a (contamination) reference genome |
| illumina_quality_kraken2_krona |
../krona/krona.cwl
(CommandLineTool)
|
Krona |
Visualization of Kraken2 report results. ktImportText -o $1 $2 |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| destination | String (Optional) | Output Destination |
Optional Output destination used for cwl-prov reporting. |
| reports_folder | Directory | Filtering reports folder |
Folder containing all reports of filtering and quality control |
| QC_forward_reads | File | Filtered forward read |
Filtered forward read |
| QC_reverse_reads | File | Filtered reverse read |
Filtered reverse read |
https://w3id.org/cwl/view/git/b9097b82e6ab6f2c9496013ce4dd6877092956a0/cwl/workflows/workflow_illumina_quality.cwl
