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![project_schema](uploads/49567b2572aa0a328fac6da2e4735f14/project_schema.png) ![project_schema](uploads/49567b2572aa0a328fac6da2e4735f14/project_schema.png)
# Links to individual tools # Links to individual tools
## [Transcript sampler](https://git.scicore.unibas.ch/zavolan_group/tools/transcript-sampler) ## [1_Transcript sampler](https://git.scicore.unibas.ch/zavolan_group/tools/transcript-sampler)
* License: MIT * License: MIT
* Rebased and merged `hugo.gillet-main-patch-48646` into main, merged `add_ci_config` into main, `Test_environment` merged into main * Rebased and merged `hugo.gillet-main-patch-48646` into main, merged `add_ci_config` into main, `Test_environment` merged into main
* Branches: `main`, `review` * Branches: `main`, `review`
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* There is an issue with one of the packages ([link](https://github.com/openvax/gtfparse/issues/36) that is breaking the whole tool, fixed it by downgrading package version * There is an issue with one of the packages ([link](https://github.com/openvax/gtfparse/issues/36) that is breaking the whole tool, fixed it by downgrading package version
* Added CI workflow, added `setup.py`, CLI is executable now and arguments are available * Added CI workflow, added `setup.py`, CLI is executable now and arguments are available
## [Transcript structure generator](https://git.scicore.unibas.ch/zavolan_group/tools/transcript-structure-generator) ## [2_Transcript structure generator](https://git.scicore.unibas.ch/zavolan_group/tools/transcript-structure-generator)
* License: MIT * License: MIT
* Branch ´andri.fraenkl-main-patch-95359´ was refactored, CI cleaned up and merged into `main`, two branches remain: `main` and `review` * Branch ´andri.fraenkl-main-patch-95359´ was refactored, CI cleaned up and merged into `main`, two branches remain: `main` and `review`
* No open issues, review MR has 32 unresolved threads, but most seem to be incorporated * No open issues, review MR has 32 unresolved threads, but most seem to be incorporated
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* There is a conda env for the tool * There is a conda env for the tool
* Docker image available * Docker image available
## [Transcript sequence extractor](https://git.scicore.unibas.ch/zavolan_group/tools/transcript-sequence-extractor) ## [3_Transcript sequence extractor](https://git.scicore.unibas.ch/zavolan_group/tools/transcript-sequence-extractor)
* License: MIT * License: MIT
* branches: Master and review, CJ deleted branch `revert-f9360ffe` as it only undid some formatting in the README, presumably as an exercise * branches: Master and review, CJ deleted branch `revert-f9360ffe` as it only undid some formatting in the README, presumably as an exercise
* suggestions from the review branch seem to have been incorporated * suggestions from the review branch seem to have been incorporated
* two parts: gtf-processing and sequence_extractor; in between there should be a call to bedtools, which is apparently missing * two parts: gtf-processing and sequence_extractor; in between there should be a call to bedtools, which is apparently missing
## [Priming site predictor](https://git.scicore.unibas.ch/zavolan_group/tools/priming-site-predictor) ## [4_Priming site predictor](https://git.scicore.unibas.ch/zavolan_group/tools/priming-site-predictor)
* License: MIT * License: MIT
## [cDNA generator](https://git.scicore.unibas.ch/zavolan_group/tools/cdna-generator) ## [5_cDNA generator](https://git.scicore.unibas.ch/zavolan_group/tools/cdna-generator)
* License: MIT * License: MIT
* This tool needs some work * This tool needs some work
* `setup.py` available, tool can be installed with `pip install .` and is executable, CLI arguments are available but CLI doesn't seem to work yet * `setup.py` available, tool can be installed with `pip install .` and is executable, CLI arguments are available but CLI doesn't seem to work yet
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* CI is partially available, tests run * CI is partially available, tests run
* Docker image available * Docker image available
## [Terminal fragment selector](https://git.scicore.unibas.ch/zavolan_group/tools/terminal-fragment-selector) ## [6_Terminal fragment selector](https://git.scicore.unibas.ch/zavolan_group/tools/terminal-fragment-selector)
* License: MIT * License: MIT
* Two branches: `main` and `review` * Two branches: `main` and `review`
* No open issues, only one unresolved thread (minor) on review MR * No open issues, only one unresolved thread (minor) on review MR
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* Tests work, CI workflow is available and works * Tests work, CI workflow is available and works
* Updated tool with CLI, also fixed the issue during executation, tool runs now * Updated tool with CLI, also fixed the issue during executation, tool runs now
## [Read sequencer](https://git.scicore.unibas.ch/zavolan_group/tools/read-sequencer) ## [7_Read sequencer](https://git.scicore.unibas.ch/zavolan_group/tools/read-sequencer)
* License: MIT * License: MIT
* Three branches: `main`, `review` and `seq_generator_implementation` for macOS implementation * Three branches: `main`, `review` and `seq_generator_implementation` for macOS implementation
* One open issue related to nextflow implementation, review MR has 2 minor unresolved threads * One open issue related to nextflow implementation, review MR has 2 minor unresolved threads
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