Q2QualityCheck

Qiime2QualityCheck class.

This task examines the quality of the metabarcoding sequences using the function demux summarize from Qiime2. Both paired-end and single-end sequences can be used, but sequences have to be demultiplexed first. It generates interactive positional quality plots based on randomly selected sequences, and the quality plots present the average positional qualities across all of the sequences selected. Default parameter is used, i.e. 10,000 random sequences are selected to generate quality plots.

More information here https://docs.qiime2.org/2022.8/plugins/available/demux/summarize/

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

- metadata file must follow a specific nomenclature when columns are tab separated. The gws_ubiome task 'Qiime2 metadata table maker' automatically generates a ready-to-use
metadata file when given a fastq folder as input. You can also upload your own metadata file.

    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