Open
Conversation
* 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
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.