Qiime2 metadata table maker

Typing name : TASK.gws_ubiome.Qiime2MetadataTableMaker

Brick : gws_ubiome

Create a metadata table (tab separator) from a fastq folder

Qiime2MetadataTableMaker class.

[Mandatory]: - fastq_folder must contains all fastq files (paired or not).

- Create metadata table from a fastq folder. User can add metadata information in a tab formated table after the first three columns:

    For paired-end files :
        #author:
        #data:
        #project:
        #types_allowed:categorical or numeric
        #metadata-type  categorical categorical
        sample-id   forward-absolute-filepath   reverse-absolute-filepath
        sample-1    sample0_R1.fastq.gz  sample1_R2.fastq.gz
        sample-2    sample2_R1.fastq.gz  sample2_R2.fastq.gz
        sample-3    sample3_R1.fastq.gz  sample3_R2.fastq.gz

    For single-end files :
        #author:
        #data:
        #project:
        #types_allowed:categorical or numeric
        #metadata-type  categorical
        sample-id   absolute-filepath
        sample-1    sample0.fastq.gz
        sample-2    sample2.fastq.gz
        sample-3    sample3.fastq.gz

Input

Folder_folder

FASTQ folder

Fastq folder

Output

Metadata_file

Metadata file

File

Configuration

sequencing_type

Optional

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

Type : string

Allowed 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 : 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

metadata_file_name

Optional

Choose an output metadata file name

Type : string

Default value : metadata.txt

Input

Output

Configuration

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