njbernstein

Count matrix with and without lammano workflow

3

Hi there, If I run the same data through `kb` with and without `--workflow lammano` and of course the necessary associated files should I get back the same exact count...

It would be great if bcftools stats could generate this output as well. I dont see it in the docs nor when I use bcftools stats. Tool works great though...

Incorrect shapes

1

Job errored out while writing results: ``` /var/spool/slurm/d/job15231496/slurm_script: 8: /var/spool/slurm/d/job15231496/slurm_script: source: not found /home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/sklearn/ensemble/weight_boosting.py:29: DeprecationWarning: numpy.core.umath_tests is an internal NumPy module and should not be imported. It will be removed...

err and out. files: ``` --------------------------------------------------------- ---------- S I G N A T U R E A N A L Y Z E R ---------- --------------------------------------------------------- * Creating output dir...

Implement a proper logger

1

Implement a proper logger. Print statements aren't great

Create notebook showing how to use and the benefits of Solo

1

cc: @vjojic

Add batching to Solo

2

currently, users must manually break up their dataset if it contains multiple sample. We can help them by running Solo for them per batch. The main issue with this is...

Hi there I used Cromwell to kick off a batch of jobs using this [workflow](https://github.com/gatk-workflows/gatk4-somatic-snvs-indels/blob/master/mutect2.wdl) I killed the Cromwell job but the genomics api is continuing to spin up VM...

Advice about running on gcs?

1

Hi there, Do you have any advice about running needlestack on a large number of samples on google cloud? Any chance you have a config already for it? Do all...