Nikos Karaiskos
Nikos Karaiskos
Example: ``` 4937 Dec 5 11:24 cutadapt.log 991 Dec 5 11:08 fastq_to_uBAM.log 0 Dec 5 13:53 genome.STAR.bamstats.log 0 Dec 5 13:53 not_genome.STAR.bamstats.log 0 Dec 5 14:13 not_rRNA.bowtie2.bamstats.log 0 Dec 6...
```/lib/python3.10/site-packages/spacemake/snakemake/main.smk:770: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.```
There's currently no functionality for that: ``` $ spacemake projects update_sample usage: spacemake projects update_sample [-h] --project_id PROJECT_ID --sample_id SAMPLE_ID [--barcode_flavor BARCODE_FLAVOR] [--adapter_flavor ADAPTER_FLAVOR] [--species SPECIES] [--map_strategy MAP_STRATEGY] [--puck PUCK]...
There's currently a `for` chunk that iterates over all pucks, one by one. Enable parallelism for that -- can be potentially solved directly in the `quant.py`.
Minor bug fix to have support for different matplotlib versions. @enessenel have a look and add any other minor commits you might have.
It's probably already deprecated in current `pandas` versions (we pin it) ``` /miniconda3/envs/spacemake/lib/python3.10/site-packages/spacemake/snakemake/main.smk:691: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use...
It's currently computed from the STAR input reads and not from the total reads as it should. (Eventually migrate to python qc sheets anyway)
Hi, thank you very much for the package. Could you comment on the running times? I cloned the repo and ran the `train_models MNIST`, it loads the dataset and starts...