Publication dateMar 9, 2022
Confidentiality public Public
timer
8 minutes, 4 seconds
Typing name : TASK.gws_omix.Fastp Brick : gws_omix Adapters removal with fastp
This task trims adapters and low-quality bases using fastp for FASTQ datasets defined by a metadata TSV. Provide a fastq_folder
(base path for relative file references) and a metadata file that is either single-end (contains absolute-filepath)
or paired-end (contains both forward-absolute-filepath and reverse-absolute-filepath).
Key options: - threads
- Forward_separator/Reverse_separator (suffixes like 1/2),
- five_prime_hard_trimming_read_size (bases trimmed from the 5′ end applied to both mates in PE).
The task auto-resolves relative paths against fastq_folder, executes fastp, and returns a FastqFolder pointing to the result directory.
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Input
FASTQ folder
Folder containing raw FASTQ(.gz); relative paths in metadata start from here
Metadata (TSV)
Table with absolute-filepath (SE) or forward- & reverse-absolute-filepath (PE)
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Output
Trimmed FASTQ
Folder with *_trimmed*.fastq.gz files
settings
Configuration
Type : intDefault value : 4 Forward_separator
Optional
string Reverse_separator
Optional
string five_prime_hard_trimming_read_size
Optional
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