Chase Clark

Figure out the easiest way to use an additional profile (or maybe make it an integrated profile option). Details on nf-core profiles can be found here: https://nf-co.re/usage/tutorials/step_by_step_institutional_profile Example: ``` params...

Since we do not have a functioning singularity profile, should we remove this as an example? _Originally posted by @WiscEvan in https://github.com/KwanLab/Autometa/pull/157#r636244595_

> Consider adding at least minimum versions for the Conda install libraries

1

> Consider adding at least minimum versions for the Conda install libraries We've listed our required libraries in `requirements.txt`. If you know of any explicit minimum versions currently required, feel...

Package version number needs to be bumped to reflect github release version number

2

Release is 1.1.9 Package is 1.1.8

Fixes issue where formula with atom counts containing a zero result in parse error for example: Works: https://massql.gnps2.org/parse?query=QUERY%20MS2DATA%20WHERE%20MS1MZ=formula(C1) Doesn't work: https://massql.gnps2.org/parse?query=QUERY%20MS2DATA%20WHERE%20MS1MZ=formula(C10)

Update to nf-core last v2 version; incorporating GTDB

18

Old and new work on updating the nf-core standardization, along with incorporating the GTDB code that hadn't been added to the Nextflow workflow

PCA behavior

3

Would it be okay to switch: https://github.com/KwanLab/Autometa/blob/0d9028cf7bad20d6e28667aaba9d3889a15ace09/autometa/common/kmers.py#L601-L607 to adapt to a lower pca dimension when there aren't enough contigs/kmers ```python if n_components > pca_dimensions and pca_dimensions != 0: if n_samples...