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- branch does NOT work
…d main nextflow files to integrate in the pipeline
… as in modules main.nf
…ig , corrected process
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tested that the branch works in this seqera run |
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Note that to plot the groups they should be parsed in seqera as this:
When groups are set up in other format it will use only the first group for comparisons (in this case "BLADDER_LOCATION"):
Checked in this run |
m-huertasp
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Feb 25, 2026
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Hola!! I think this is quite a nice job! As we talked about, there are a few things that might need to be changed. I have added some comments so it is easier to check the things we discussed.
Good job!
Co-authored-by: Marta Huertas <97596516+m-huertasp@users.noreply.github.com>
…s parameter, and the output of a pdf with all plots per group. Also added a condition so this module can only run when user defines a groups list
efigb
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Feb 25, 2026
efigb
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Feb 25, 2026
…ALL_GENES values per group. Added new input in config for it. Also fixed bug in processing groups and added in modules.config a subdirectory for output
efigb
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Feb 26, 2026
efigb
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Feb 26, 2026
efigb
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Feb 26, 2026
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tested branch in pipeline with seqera and works |
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This branch adds a new module to process analysis of consensus exons depth for a defined group of samples and for a subset of genes (default genes in the panel) plotting all these possibilities in an output pdf that is stored in the same output directory as plotting the depths (
/depths/summary)