home.md

@@ -19,7 +19,7 @@
 ![project_schema](uploads/49567b2572aa0a328fac6da2e4735f14/project_schema.png)
 
 # 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
 * Rebased and merged `hugo.gillet-main-patch-48646` into main, merged `add_ci_config` into main, `Test_environment` merged into main
 * Branches: `main`, `review`
@@ -28,7 +28,7 @@
 * 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
 
-## [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
 * 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
@@ -36,16 +36,16 @@
 * There is a conda env for the tool
 * 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
 * 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
 * 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
 
-## [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
 * 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
@@ -54,7 +54,7 @@
 * CI is partially available, tests run
 * 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
 * Two branches: `main` and `review`
 * No open issues, only one unresolved thread (minor) on review MR
@@ -62,7 +62,7 @@
 * Tests work, CI workflow is available and works
 * 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
 * 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