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Got the following issue during the visualisation tutorial Error in library(cowplot) : there is no package called 'cowplot' \ and in the installation guide there is no indication to install the package so maybe should be included there.

• add information about customizing the pipeline
• check links to config file yml are working for all the tutorials
• clarify customization of path to conda if avail, sample_qc and qc_genelist.csv file

what to do when the pipeline breaks mid-run: sometimes the pipeline will stop because a parameter is wrong in the config file or because of any small issue in the yml such as the wrong path for a certain file. We recommend checking the log file for information on what exactly failed. After fixing the issue we recommend cleaning the project folder of any intermediate files, to allow a proper re-run.

DendrouLab/panpipes#162

The four ingestion tutorials have a "longer" version of the config file yml.
we need to align them to the new config file here https://github.com/DendrouLab/panpipes/blob/main/panpipes/panpipes/pipeline_ingest/pipeline.yml

files to modify:

• https://github.com/DendrouLab/panpipes-tutorials/blob/main/docs/ingesting_multiome/pipeline.yml
• https://github.com/DendrouLab/panpipes-tutorials/blob/main/docs/ingesting_multimodal_data/pipeline.yml
• https://github.com/DendrouLab/panpipes-tutorials/blob/main/docs/ingesting_mouse/pipeline.yml
• https://github.com/DendrouLab/panpipes-tutorials/blob/main/docs/ingesting_data/pipeline.yml

https://github.com/DendrouLab/panpipes-tutorials/blob/main/docs/index.md

Hello,
I run the command: panpipes ingest config and dot this error:
RuntimeError: This version of jaxlib was built using AVX instructions, which your CPU and/or operating system do not support. You may be able work around this issue by building jaxlib from source.
Thank you,

Just as a reminder for myself to adapt the prefilled pipeline.yml for the preprocess tutorial as soon as the respective PR is merged.

• Update tutorial pipeline.yml
• Update pipeline.yml sections shown in the tutorial itself

Scatter color function is not working and it can't recognize any inputs (even a hex colour code).
Tried changing the pair_scatters_markers.csv colour indication to rna:douplet_scores, douplet_scores and a hex code and all of them errored
The first two features are read fine but not the third one.
Tested in python environment with mu.pl.scatter function and same error appeared.
Also tested following error suggestion of doubling the rna:rna:doublet_scores and same issue appeared again.
Additionally tested with the sc.pl.scatter function in a python environment using simple gene markers and color as doublet_scoresand it worked so it must be a muon issue.
Additionally no instruction on how to accurately create the input file for scatter plots on the visualisation workflow or the gene format list.

Clustering issue for atac as it requires a signac_norm layer however during the preprocessing steps atac is normalised via normalize: log1p
So as a result we have a logged_counts layer rather than a signac_norm one which causes the clustering pipeline tutorial to fail.

As discussed, we want to remove the specified conda environment paths from the prefilled tutorial pipeline.yml files, as they cause the workflow to crash when run by the user. Specifically, we need to do the following:

• Go through all tutorial pipeline.yml files (they should be linked on top of the respective parameter explanation file) and remove any specified conda environment paths
• Add a sentence in each tutorial explaining how to specify the conda environment

DendrouLab/panpipes#163

Pipeline.yml from the tutorial has an option in the total VI filter_adt_outliers however that does not allow it to run properly. The tutorial git yml (pipeline_integration.yml) shows an outdated version, however the panpipes git yml has an updated version which fixes the issue by replacing it with filter_prot_outliers. So tutorial yml should be updated as well

Vis python script does not make the scatters directory that is required in the tutorial pipeline.yml so it errors.
So for visualisation to run user needs to manually create a new directory inside /vis/data called scatters.

Downloaded files from tutorial paired_scatter, custom_markers indicate prot_CD8, however the teaseq_clusterd.h5mu file created during clustering presents with prot_CD8a so during visualisation it can't find the correct prot_CD8.
Protein name in the downloaded files from the visualisation tutorials has to be changed to prot_CD8a

For the section "Filtering data with panpipes - running the pipeline"

The pre-filled pipeline.yml file (here) contains an error on the specificed ATAC normalisation method, and needs to be updated.

# ATAC preprocessing steps
# ------------------------
atac:
  binarize: False
  normalize: TFIDF  #"log1p" or "TFIDF"

The figures generated using this pre-filled pipeline.yml do not match the PCA plot images posted in the documentation. This is because the pre-filled YAML file uses TFIDF, but the plot images were generated using log1p .