gaow

Sidebar toggle

1

Hi Anika, I recently adopted writr to replace the [cokowiki](https://www.dokuwiki.org/template:codowik) theme. writr is great! But there is one feature I miss of codowiki: the sidebar toggle. Would it be possible...

Indentation interferes with syntax highlighting

4

I"m using `report` action to dump some utility functions, see below:  Not sure how hard it is but it would be real nice to add some argument in `report`...

How to add colors to github preview

2

Our notebook, particularly when containing long scripts, can be [a bit ugly](https://github.com/stephenslab/gtexresults/blob/master/workflows/fastqtl_to_mash.ipynb). Even though those with [shorter scripts](https://github.com/TADA-A/TADA-A/blob/master/external_tools/mutation_annotation_pipeline.ipynb) are fine. But other notebooks on github seems to show better: https://github.com/geekypete/Genomic-Prediction/blob/master/GenomicPrediction.ipynb...

Multi-column preview of multiple images in the main notebook

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I'm wondering if it is possible to make preview in main notebook configurable. Currently it is taking the entire width of the cell which does not look very nice. Even...

%sessioninfo magic should add versions to depended packages

9

Eg, if I have a workflow step in a notebook: ``` [flash] depends: R_library("stephenslab/flash") ``` Then it should not be too much to ask `%sessioninfo` to display an R session...

Sparse logistic regression with spike slab prior example

29

I am trying to adapt #154 to using a spike-slab prior `pi * delta + (1 - pi) * N(mu, sigma)` where pi, mu and sigma are given and a...

Support to DNAnexus applet

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@BoPeng we are recently looking into UKB data for some traits we analyze, https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/guide-to-analyzing-large-sample-sets the new UKB release is only available through this platform (!!). As you can see, the...

False alarm on failed tasks

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I've got in my simulation runs: ``` WARNING: Task M20_b38d872198d6c6d4 inactive for more than 85 seconds, might have been killed. INFO: 19 of 20 tasks in M20_b38d872198d6c6d4 failed ``` But...

Here is how currently benchmark workflows are automatically generated: https://github.com/gaow/random-nbs/blob/master/slides/20191201_DSC_SoS/sos/test_run.sos The two key elements in the design are: 1. Pre-specified input and output file names and `group_by` 2. Dependency by...

Change of configuration file triggers rerun even if it has no impact on the pipeline

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Here is a MWE. I have a script called `test.sos`: ``` [1] output: CONFIG['input'] run: touch ${output} [2] input: CONFIG['input'] output: CONFIG['output'] task: workdir = './', concurrent = True run:...