zavolanlab / zarp-cli

A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
https://zavolanlab.github.io/zarp-cli/
Apache License 2.0
4 stars 1 forks source link

feat: fetch genome resources and set paths #61

Closed uniqueg closed 1 year ago

uniqueg commented 1 year ago

Please include a summarized description of the change(s) and which issue(s) this pull request addresses, if any. Please include relevant motivation and context, unless already duly described in an associated issue or resource. Make sure to list any dependencies that are required for this change.

Fixes #25

Type of change

Checklist

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (56fe68f) 100.00% compared to head (052af7a) 100.00%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## dev #61 +/- ## ========================================= Coverage 100.00% 100.00% ========================================= Files 22 22 Lines 1071 1151 +80 ========================================= + Hits 1071 1151 +80 ``` | [Impacted Files](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab) | Coverage Δ | | |---|---|---| | [zarp/abstract\_classes/sample\_processor.py](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-emFycC9hYnN0cmFjdF9jbGFzc2VzL3NhbXBsZV9wcm9jZXNzb3IucHk=) | `100.00% <100.00%> (ø)` | | | [zarp/cli.py](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-emFycC9jbGkucHk=) | `100.00% <100.00%> (ø)` | | | [zarp/config/args.py](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-emFycC9jb25maWcvYXJncy5weQ==) | `100.00% <100.00%> (ø)` | | | [zarp/config/mappings.py](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-emFycC9jb25maWcvbWFwcGluZ3MucHk=) | `100.00% <100.00%> (ø)` | | | [zarp/config/models.py](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-emFycC9jb25maWcvbW9kZWxzLnB5) | `100.00% <100.00%> (ø)` | | | [zarp/config/parser.py](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-emFycC9jb25maWcvcGFyc2VyLnB5) | `100.00% <100.00%> (ø)` | | | [zarp/plugins/sample\_fetchers/sra.py](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-emFycC9wbHVnaW5zL3NhbXBsZV9mZXRjaGVycy9zcmEucHk=) | `100.00% <100.00%> (ø)` | | | [zarp/plugins/sample\_processors/genomepy.py](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-emFycC9wbHVnaW5zL3NhbXBsZV9wcm9jZXNzb3JzL2dlbm9tZXB5LnB5) | `100.00% <100.00%> (ø)` | | | [zarp/samples/sample\_record\_processor.py](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-emFycC9zYW1wbGVzL3NhbXBsZV9yZWNvcmRfcHJvY2Vzc29yLnB5) | `100.00% <100.00%> (ø)` | | | [zarp/utils.py](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-emFycC91dGlscy5weQ==) | `100.00% <100.00%> (ø)` | | | ... and [1 more](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/61?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab) | |

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