Publication dateMar 9, 2022
Confidentiality public Public
Typing name : TASK.gws_omix.TrimGalore Brick : gws_omix This task uses Trim_galore to clip and trimmed your sequencing datasets
TrimeGalore class.
Configuration options
"quality": IntParam(default_value=20, min_value=1, max_value=40, short_description="Trim low-quality ends from reads in addition to adapter removal. Quality score in Phred (see https://en.wikipedia.org/wiki/Phred_quality_score) [Default: 20]"),
"paired_end": StrParam(default_value="YES",allowed_values=["YES","NO"], short_description="Sequencing strategy: paired-end file (forward reads (sample_XXX_1.fq) and reverse reads (sample_XXX_2.fq)) or not--paired. [Default: YES]"),
"threads": IntParam(default_value=2, min_value=1, short_description="Number of threads"),
"filter_reads_with_unsequenced_nucl": IntParam( default_value=100, short_description="The total number of Ns (as integer) a read may contain before it will be removed altogether. In a paired-end setting, either read exceeding this limit will result in the entire pair being removed from the trimmed output files."),
"output_dir": StrParam(default_value="filtered_reads", short_description="Name of the output directory, which contained trimmed files and report files")
settings
Configuration
Number of threads
Type : intDefault value : 2Trim low-quality ends from reads in addition to adapter removal. Quality score in Phred (see https://en.wikipedia.org/wiki/Phred_quality_score) [Default: 20]
Type : intDefault value : 20Minimum reads size
Type : intDefault value : 10Type of sequencing strategy [Respectively, options : paired-end, single-end]. Default = paired-end
Type : stringAllowed values : paired-end single-end Default value : paired-end forward_file_differentiator
Optional
Paired-end sequencing forward file name differanciator, e.g: sample-A_R1.fastq.gz
Type : stringDefault value : _R1 reverse_file_differentiator
Optional
Paired-end sequencing forward file name differanciator, e.g: sample-A_R2.fastq.gz
Type : stringDefault value : _R2 filter_reads_with_unsequenced_nucl
Optional
The total number of Ns (as integer) a read may contain before it will be removed altogether. In a paired-end setting, either read exceeding this limit will result in the entire pair being removed from the trimmed output files.
Type : intDefault value : 100Technical bricks to reuse or customize
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