Fix/fix preprocessing 20211119 #9
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* R1/R2 lengths are now assessed and homogenised separately (i.e. they can have different lengths as supported by Figaro) * initial read length distribution assessment is now performed by fastqc * fastq filenames are normalised to R1/R2 naming scheme * removed pair_id from sample meta information
added gaga2 workflow diagram
added workflow diagram
…lab/gaga2 into feature/add_preprocessing
* paired-end reads are now filtered by whether they're spanning the amplicon length (figaro-requirement) * single-end reads are not filtered
* fixed issue with homogeneous length trimming * removed check for preprocessed reads that would prevent preprocessing for 'garbage' data
* read length distributions are now obtained from bbduk histograms (non-binned) * experimental: allow shorter reads instead of forcing to completely cover amplicon
* version 0.5 * if reads are not covering the full amplicon size, a shortened amplicon size is provided to figaro (experimental) * bbduk length histograms (instead of fastqc) are now provided to read length assessment * sample classification was (temporarily?) moved into the fastq-collection Channel (due to issues with nf 21.10+) * resolved a data flow issue that would allow dada2 processes to start before the preprocessing is finished
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