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CSV tests need to point to nf-core repository #9

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atrigila opened this issue Mar 19, 2024 · 0 comments · Fixed by #15
Closed

CSV tests need to point to nf-core repository #9

atrigila opened this issue Mar 19, 2024 · 0 comments · Fixed by #15
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@eugeniafontecha
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bug Something isn't working good first issue Good for newcomers

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@atrigila
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Description of the bug

While the current testing of the pipeline works, the CSVs are not stored in the nf-core repository. This should be corrected for reproducibility issues.

Example phaseimpute/tests/csv:

sample,vcf,csi
NA12878,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA12878/NA12878.s.1x.bcf,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA12878/NA12878.s.1x.bcf.csi
NA19401,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA19401/NA19401.s.1x.bcf,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA19401/NA19401.s.1x.bcf.csi
NA20359,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA20359/NA20359.s.1x.bcf,https://raw.githubusercontent.com/louislenezet/test-datasets/imputation/data/individuals/NA20359/NA20359.s.1x.bcf.csi

Command used and terminal output

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Relevant files

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@atrigila atrigila added the bug Something isn't working label Mar 19, 2024
@atrigila atrigila moved this to To do in Hackathon: May 2024 Mar 19, 2024
@atrigila atrigila added the good first issue Good for newcomers label Mar 19, 2024
@atrigila atrigila moved this from To do to In progress in Hackathon: May 2024 Mar 19, 2024
@atrigila atrigila linked a pull request Mar 19, 2024 that will close this issue
Csv files point to nf-core repository #15
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Csv files point to nf-core repository eugeniafontecha/phaseimpute
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@atrigila @eugeniafontecha