Carl Mathias Kobel

Error in passthrough argument feature: `Invalid config definition: Config entry must start with a valid identifier.`

4

When using the passthrough argument feature (e.g. by setting prokka's --kingdom argument to "archaea") on a fresh installation of CompareM2, the following error message might show: ``` $ comparem2 --dry-run...

v2.11.1 ``` thylakoid@johans results_comparem2 $ cat samples/116_2/prokka/ 116_2.err 116_2.fna 116_2.gff 116_2.sqn 116_2.txt 116_2.faa 116_2.fsa 116_2.gff_nofasta 116_2.tbl .software_version.txt 116_2.ffn 116_2.gbk 116_2.log 116_2.tsv thylakoid@johans results_comparem2 $ cat samples/116_2/prokka/.software_version.txt thylakoid@johans results_comparem2 $ ```...

These jobs run when there is no input

1

For example: ```bash comparem2 --config input_genomes="path/to/my/genomes_*.fna" --until fast ``` This path clearly does not exist so no jobs should be run. ``` Job stats: job count -------------- ------- assembly_stats 1...

No need to re-compute analyses that have already been completed for said input genomes. https://snakemake.readthedocs.io/en/stable/executing/caching.html

Another thing is that I wish that comparem selects $COMPAREM2_DATABASES/{version_major}.{version_minor}/ ... instead of just using the environment variable base. This way you can have multiple versions installed without database conflicts,...

Seems like ncbi genomes don't have GFF-annotations when the completeness (checkm2) is below ~80. So now I'm just considering if there should be a way of handling this. For now...

Report graphics should work with <= 512 genomes

1

512? Easy fix. Make a test that checks that all figures look alright with 1, 2, 20, 50, 100, 500 ...

Differentiate rule gather

7

I'm actually considering going back to the old system where the ncbi accessions had their own rule. Then it can also pool (run quicker) and have its own environment. The...

`--test`

2

Could be a nice and easy way to check that everything is working.

Self-contained docker image?

1

It suddenly struck me that you need to install conda (mamba) and the CompareM2 conda package when using the docker image. Wouldn't it be better to have a self-contained docker...