Omkar Mohite

Feature request phylogenetic analysis subworkflow

2

I think it would be valuable to create a phylogenetic tree sub workflow. 1. autoMLST-based tree 2. GTDB tree using [de_novo_wf](https://ecogenomics.github.io/GTDBTk/commands/de_novo_wf.html) 3. Roary core genome alignment tree Perhaps we can...

Suggestions for documentation

18

I am creating an issue to list any feedback we get on improving documentation here. - [x] Provide warning and guide to install gcc. Many machine don't have gcc installed...

This common error was also found in BGC workflow when the list of BGCs in the sample set it too high. `/datadrive/bgcflow/.snakemake/shell_tmp.iz1795my/script.sh: line 10: /datadrive/bgcflow/.snakemake/conda/c2ac5875f1b6f2374bfd4dbe39acdefe_/bin/python: Argument list too long `...

Error in running bigslice rule: Not in index, query string too large

3

``` run_status is now FEATURES_EXTRACTED Building GCF models... Dumping in-memory database content into /datadrive/data2/bgcflow/data/processed/strepto_combine/bigslice/cluster_as_6.1.1/result/data.db... Traceback (most recent call last): File "/datadrive/data2/bgcflow/.snakemake/conda/c53188cf74abfdc284d24b807d803856_/bin/bigslice", line 1828, in main clustering = BirchClustering.run( ^^^^^^^^^^^^^^^^^^^^ File...

Some of the datasets I worked with were very diverse. Sketch sampling size is a key parameter for diverse dataset and accurate predictions. I increase the sketch size with option...

New rules: BAGEL

2

I think it could be nice to also include BAGEL or other RiPP-specific tools as rules in the next versions.

Feat: Pangenome graph module

2

This is a request for a new feature rule to use PPanGGOLiN to create pagenome graphs for the genome projects. I think we should use the Roary-defined Gene Famillies as...

BiG-SLICE and BiG-SCAPE integration strategy

2

For projects with too large number of BGCs, BiGSLICE is the preferred choice. However, I wanted to discuss a potential strategy to run BiGSLICE first to get first degree of...

This is one suggestion to include BGCFlow on the SMBP portal. We can possibly add several example studies/ papers on the website too. https://www.secondarymetabolites.org/

The BiGSCAPE output HTML report is empty. Consider using `--mix` parameter in the bigscape rule as `--no_classify` was used.