Fix/virsorter2 #135
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Fix/virsorter2 #135
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KateSakharova
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mberacochea
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Nov 6, 2024
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Thanks @KateSakharova. A massive chunk of work. I left a few comments, but I think it's pretty close to completion IMO
.github/workflows/unit_tests.yml
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| - name: Install dependencies | ||
| run: | | ||
| pip install -r requirements-test.txt | ||
| pip install --upgrade numpy pandas |
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Please bump these 2 dependencies in requirements-test.txt
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pandas is there, numpy included with pandas installation
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alright.. then bump the pandas version
mberacochea
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Nov 8, 2024
modules/local/virsorter2/main.nf
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| script: | ||
| def args = task.ext.args ?: '' | ||
| """ | ||
| # speed up hmmsearch |
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| # speed up hmmsearch | |
| # Settings to speed up hmmsearch | |
| # TODO: this needs to be tested, it doesn't seem to speed up so we decided to chunk the fasta instead |
.github/workflows/unit_tests.yml
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| - name: Install dependencies | ||
| run: | | ||
| pip install -r requirements-test.txt | ||
| pip install --upgrade numpy pandas |
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alright.. then bump the pandas version
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Re-used PR #128
VirSorter2 is default tool. Pipeline can also run VirSorter1 using flag
--use_virsorter_v1Input is chunked for VirSorter2. Seems there is no easy way to parallel it jiarong/VirSorter2#218
Criteria for HC and LC is weird. It is required further discussion