Work-in-progress
Workflow for read quality control and trimming.
Steps:
- FastQC (read quality control)
- fastp (read quality trimming)
- bbduk used for rrna filtering
Inputs
ID | Name | Description | Type |
---|---|---|---|
threads | number of threads | number of threads to use for computational processes | int? |
memory | maximum memory usage in megabytes | maximum memory usage in megabytes | int? |
filter_rrna | n/a | n/a | boolean |
forward_reads | forward reads | forward sequence file locally | File |
reverse_reads | reverse reads | reverse sequence file locally | File |
step | CWL base step number | Step number for order of steps | int? |
Steps
ID | Name | Description |
---|---|---|
fastqc | FastQC | Quality assessment and report of reads |
fastp | fastp | Read quality filtering and (barcode) trimming. |
bbduk | rrna filter (bbduk) | Filters rrna sequences from reads using bbduk |
fastqc_files_to_folder | FastQC output | Preparation of FastQC output files to a specific output folder |
filtered_files_to_folder | fastp output | Preparation of fastp output files to a specific output folder |
bbduk_files_to_folder | fastp output | Preparation of rrna-filter (bbduk) output files to a specific output folder. Contains fwd/rev reads stats and summary file. |
Outputs
ID | Name | Description | Type |
---|---|---|---|
files_to_folder_fastqc | FASTQC | Quality reporting by FASTQC | Directory |
files_to_folder_filtered | Filtered reads folder | Output folder with filtered reads, stats and reports. | Directory |
QC_forward_reads | Filtered forward read | Filtered forward read with fastp and (optionally) rrna filtered. | File |
QC_reverse_reads | Filtered reverse read | Filtered reverse read with fastp and (optionally) rrna filtered. | File |
Version History
Version 1 Created 22nd Dec 2020 at 16:27 by Bart Nijsse
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