TrimGalore cleaning - gws_omix

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")

Input

Fastq folder

Output

Resource set

File

Configuration

threads

Optional

Number of threads

Type : int

Default value : 2

quality

Optional

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]

Type : int

Default value : 20

min_size

Optional

Minimum reads size

Type : int

Default value : 10

sequencing_type

Optional

Type of sequencing strategy [Respectively, options : paired-end, single-end]. Default = paired-end

Type : string

Default value : paired-end

forward_file_differentiator

Optional

Paired-end sequencing forward file name differanciator, e.g: sample-A_R1.fastq.gz

Type : string

Default value : _R1

reverse_file_differentiator

Optional

Paired-end sequencing forward file name differanciator, e.g: sample-A_R2.fastq.gz

Type : string

Default 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 : int

Default value : 100