Tim Booth
Tim Booth
Hi, I'm currently working on visualising the output of Cutadapt in MultiQC, which basically entails using the summary table info to render a histogram. There is an existing module for...
Still looking into this, and whether it is really a problem with my chosen container, but here is the initial error: ``` tbooth@balisaur[tbooth] docker info Containers: 0 Images: 0 Storage...
If no `--region` is specified on the command line the default is hard coded to 'us-east-1'. The region set in the profile is ignored, and also the standard `AWS_DEFAULT_REGION` environment...
The current advice from ONT regarding how to perform duplex basecalling is here: https://community.nanoporetech.com/posts/guppy-v6-0-0-release (dated 6th December 2021 - login required to view) It makes no mention of duplex-tools, but...
Snakemake now has a lovely green logo, but the files found under the images directory in the source contain the old logo. Could the new logo be added to the...
From @jdblischak Snakemake 7.8 introduced a few big changes. Your tutorial is based on version 5.32.2. You have a box in the episode "How Snakemake plans what jobs to run"...
from @tkphd Two editors are mentioned here, but no editor is invoked in the lesson material. Throughout, when showing changes to a file, preface it with the command the instructor...
from @tkphd Conda is a common and useful tool, but it is simply invoked, not introduced. Explain what it is (a Python distribution with virtual environment isolation), how it helps...
From @tkphd The lesson homepage lists the following prerequisites: Familiarity with the Bash command shell, including concepts like pipes, variables and loops. Knowledge of bioinformatics fundamentals like the FASTQ file...
From @jdblischak I know you recommend using `r"""` to make the quoting more robust, but personally I find this more readable: ~~~ shell: """ fastqc -o . {input} mv {wildcards.sample}_fastqc.html...