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Create nf-tests for "fusioncatcher": "detect" and "download" modules #521

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nschcolnicov opened this issue Nov 22, 2024 · 4 comments
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@nschcolnicov
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Description of feature

Create nf-tests for "fusioncatcher" "detect" and "download" modules

@nschcolnicov nschcolnicov changed the title Create nf-tests for "fusioncatcher" "detect" and "download" modules Create nf-tests for "fusioncatcher": "detect" and "download" modules Nov 22, 2024
@atrigila
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Some notes here:

@atrigila
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atrigila commented Dec 5, 2024

Trying to download the files in an HPC resulted in #570

@atrigila
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atrigila commented Dec 5, 2024

In principle, FusionCatcher assumes the presence of complete whole-genome genomic and transcriptomic data. One could write nf-tests with a small subset of fastq files but would still need the full fusioncatcher-build reference dataset. These tests may be impractical due to the massive computational/storage requirement.

@atrigila atrigila moved this to On hold in rnafusion Dec 5, 2024
@rannick
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rannick commented Dec 6, 2024

One could build the references for chr4 or another if necessary.

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