Pablo Moreno

Workflow with collection fails to execute but works through UI

1

I have a workflow that uses dataset collections, which works through the interface, but produces an error when running through bioblend (latest installable pip version): ``` Traceback (most recent call...

Proposal: dynamic download of test data

7

I would like to propose the development of a new feature. On our CI using planemo we have some logic so that for any tool directory that has a `get_test_data.sh`...

DNS not resolved inside container tool when using --mulled_containers

2

When starting planemo with with mulled containers support I get that tools which require DNS resolution (because for instance they need to download something) cannot resolve DNS addresses. If I...

SCCAF expects the AnnData object passed to have tSNE or UMAP embeddings; if they are not available, SCCAF cli should exit with an error code. ``` INFO:root:Read ann data file:...

On occassions, cross validation will fail because sampling picks sets belonging to a single class

1

I hope I'm reading this error correctly @chichaumiau, but I guess we need to protect the cross validation from these sort of situations: if sampled set only contains a single...

plot_roc: line 1017 heatmap: line 992 ``` /usr/local/lib/python3.6/site-packages/SCCAF/__init__.py:1017: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may...

Support multiple clustering resolutions from AnnData

4

Currently our Single Cell Expression Atlas AnnData files (such as http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-MTAB-6077/E-MTAB-6077.project.h5ad) will include multiple clustering resolutions and optionally a cell_type clustering field in the obs. Currently when run it I...

MacOS X make fails at the end due to missing dylib

10

**Please, do not create duplicate issues** ### Actual behaviour On the final make command suggested for macOS in the README (after following all the mentioned installations in the README) it...

### Name of the tool cellranger multi ### Tool homepage https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov ### Tool description is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate...

Installation of newer bknn 1.6.0 package (att @ktpolanski) conflicts with numpy installation for scanpy 1.9.8: ``` The following packages are incompatible ├─ bbknn 1.6.0** is installable with the potential options...