diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index 4d99edb5190b0dfab922758bb9e3f6b7ef474fdf..0000000000000000000000000000000000000000
--- a/Dockerfile
+++ /dev/null
@@ -1,11 +0,0 @@
-FROM python:3.9-slim-buster
-
-WORKDIR /usr/src/app
-
-COPY README.md pyproject.toml ./
-ADD tsg ./tsg
-ADD data ./data
-
-RUN pip install .
-
-ENTRYPOINT [ "transcript-generator" ]
\ No newline at end of file
diff --git a/Trans_Struc_Gen.nf b/Trans_Struc_Gen.nf
deleted file mode 100644
index fa305642bca9ee695547f40d3fe3469c1670889c..0000000000000000000000000000000000000000
--- a/Trans_Struc_Gen.nf
+++ /dev/null
@@ -1,101 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl=2
-
-```c
-/*
- * Define the input parameters"""Takes input from csv-formatted file ("ID,Count")
- with counts for individual transcripts.
- Also a gtf-formatted file with exon coordinates
- of the transcripts included in the csv file.
- Outputs gtf-formatted file containing
- generated intron/exon structures per transcript.
- Outputs csv-formatted file
- ("NewTranscriptID,ID,Count") with id of
- generated transcript, id of original
- transcript (without intron inclusions) and
- Counts.
- */
-params.cvs_file = "$projectDir/tests/ #Input cvs file from group 1
-params.gtf_file = "$projectDir/tests/ #Input gtf file from group 1
-params.outdir = "results"
-
-
-/* Log some information for the user */
-
-log.info """\
- R N A S E Q - N F P I P E L I N E
- ===================================
- cvs_file : ${params.cvs_file}
- gtf_file : ${params.gtf_file}
- outdir : ${params.outdir}
- """
- .stripIndent()
-
-/*
- * define the `file_validation` process
- * given that the input files exist and are the correct format
- */
-
-process file_validation {
-
- input:
- path cvs_file
- path gtf_file
-
- output:
- path cvs_file into struc_gen
- path gtf_file into struc_gen
-
- script:
- """
-
- """
-}
-
-/*
- * Define the transcript structure generation
- * Read gtf files to define exons/introns and add random mutation coefficient.
- */
-
-process struc_gen {
-
- input:
-
-
- output:
-
-
- script:
- """
-
-
- """
-}
-
-
-
-/* Start the job:
- * initialize variables
- */
-
-Channel
- .fromFilePairs( params.reads, checkIfExists:true )
- .set { read_pairs_ch }
-
-
-/* The "main" function:
- * Use CLI arguments to create structure sequences and output text file & gtf file with selected exon structures
- */
-
-workflow {
- file_validation_ch = file_validation(params.cvs_file, params.gtf_file)
- struc_gen_ch = struc_gen( # No idea yet) }
-
-
-/* Book keeping upon workflow completion */
-workflow.onComplete {
- log.info (workflow.success ? "\nDone! Open the following report in your browser --> $params.outdir/multiqc/multiqc_report.html\n" : "Oops .. something went wrong")
- )
-}
-```
diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index bf7442174e9750f8194ac78a277fe52bbb5df5a9..0000000000000000000000000000000000000000
--- a/environment.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-name: transcript-structure-generator
-channels:
- - defaults
- - conda-forge
-dependencies:
- - python=3.9
- - matplotlib
- - pandas
- - pip
- - tqdm
- - flake8-docstrings
- - mypy
- - flake8
- - pytest
- - pylint
- - coverage
diff --git a/pyproject.toml b/pyproject.toml
deleted file mode 100644
index 6cb72f00e895998dafb67f2b07d20037ae989a09..0000000000000000000000000000000000000000
--- a/pyproject.toml
+++ /dev/null
@@ -1,25 +0,0 @@
-[project]
-name = "tsg"
-version = "0.2.0"
-authors = [
- { name="Michael Zimmermann", email="michael.zimmermann@unibas.ch" },
- { name="Andri Fraenkl", email="andri.fraenkl@unibas.ch" },
- { name="Larissa Glass", email="larissa.glass@unibas.ch" },
-]
-description = "Transcript Structure Generator"
-readme = "README.md"
-requires-python = ">=3.7"
-license = {text = "MIT"}
-dependencies = [
- "pandas",
- "tqdm",
-]
-
-[tool.setuptools]
-packages = ["tsg"]
-
-[project.urls]
-"Homepage" = "https://git.scicore.unibas.ch/zavolan_group/tools/transcript-structure-generator"
-
-[project.scripts]
-transcript-generator = "tsg.cli:app"
\ No newline at end of file