diff --git a/.zenodo.json b/.zenodo.json
deleted file mode 100644
index 9aa1f86e4367ceac3dabbbd2cb5e2ab449dc4cb1..0000000000000000000000000000000000000000
--- a/.zenodo.json
+++ /dev/null
@@ -1,24 +0,0 @@
-
-{
- "creators": [
- {
- "name": "Ozadam, Hakan",
- "affiliation": "UT, Austin, TX, USA"
- },
- {
- "name": "Cenik, Can",
- "affiliation": "UT, Austin, TX, USA"
- }
- ],
- "keywords": [
- "bioinformatics",
- "genomics",
- "ribosome",
- "ribo-seq",
- "Python"
- ],
- "description": "<p>RiboFlow is a NextFlow based pipeline for processing ribosome profiling data.</p>",
- "access_right": "open",
- "license": "MIT",
- "upload_type": "software"
-}
diff --git a/README.md b/README.md
deleted file mode 100644
index 72f5e326691cc93823d2f993e8230259117f378b..0000000000000000000000000000000000000000
--- a/README.md
+++ /dev/null
@@ -1,222 +0,0 @@
-[](https://doi.org/10.5281/zenodo.3376949)
-
-
-# RiboFlow
-
-RiboFlow is a [Nextflow](https://www.nextflow.io/) based pipeline
-for processing ribosome profiling data.
-
-## Installation
-
-### Requirements
-
-* [Nextflow](https://www.nextflow.io/)
-* [Docker](https://docs.docker.com/install/) (Optional)
-* [Conda](https://conda.io/en/latest/miniconda.html) (Optional)
-
-First, follow the instructions in [Nextflow website](https://www.nextflow.io/) and install Nextflow.
-
-The easiest way of using RiboFLow is using Docker.
-If using Docker is not an option, you can install the dependencies using Conda
-and run RiboFlow without Docker.
-
-### Docker Option
-
-Install [Docker](https://docs.docker.com/install/).
-Here is a [tutorial for Ubuntu.](https://www.digitalocean.com/community/tutorials/how-to-install-and-use-docker-on-ubuntu-18-04)
-
-All remaining dependencies come in the Docker image [ceniklab/riboflow](https://hub.docker.com/r/ceniklab/riboflow).
-This image is automatically pulled by RiboFlow when run with Docker (see test runs below).
-
-### Conda Option
-
-This option has been tested on Linux systems only.
-
-Install [Conda](https://conda.io/en/latest/miniconda.html).
-
-All other dependencies can be installed using the environment file,
-environment.yaml, in this repository.
-```
-git clone https://github.com/ribosomeprofiling/riboflow.git
-conda env create -f riboflow/environment.yaml
-```
-
-The above command will create a conda environment called _ribo_
-and install dependencies in it.
-To start using RiboFlow, you need to activate the _ribo_ environment.
-
-`conda activate ribo`
-
-## Test Run
-
-For fresh installations, before running RiboFlow on actual data,
-it is recommended to do a test run.
-
-Clone this repository in a new folder and change your working directory to the RiboFlow folder.
-```
-mkdir rf_test_run && cd rf_test_run
-git clone https://github.com/ribosomeprofiling/riboflow.git
-cd riboflow
-```
-
-Obtain a copy of the sample data in the working directory.
-```
-git clone https://github.com/ribosomeprofiling/rf_sample_data.git
-```
-
-### Run Using Docker
-
-Provide the argument `-profile docker_local` to Nextflow to indicate Docker use.
-
-`nextflow RiboFlow.groovy -params-file project.yaml -profile docker_local`
-
-### Run Using Conda Environment
-
-Make sure that you have created the conda environment, called _ribo_,
-using the instructions above. Then activate the conda environment.
-
-`conda activate ribo`
-
-If the above command fails to activate the ribo environment, try
-`source activate ribo`
-
-Now RiboFlow is ready to run.
-
-`nextflow RiboFlow.groovy -params-file project.yaml`
-
-## Output
-
-Pipeline run may take several minutes.
-When finished, the resulting files are in the `./output` folder.
-
-Mapping statistics are compiled in a csv file called `stats.csv`
-
-```
-ls output/stats/stats.csv
-```
-
-Ribosome occupancy data is in a single
-[ribo file](https://ribopy.readthedocs.io/en/latest/ribo_file_format.html) called `all.ribo`.
-
-`ls output/ribo/all.ribo`
-
-You can use
-[RiboR](https://github.com/ribosomeprofiling/ribor) or
-[RiboPy](https://github.com/ribosomeprofiling/ribopy) to work with ribo files.
-
-
-## Actual Run
-
-For running RiboFlow on actual data, files must be organized and a parameters file must be prepared.
-You can examine the sample run above to see an example.
-
-1. Organize your data. The following files are required for RiboFlow
-* **Ribosome profiling sequencing data:** in gzipped fastq files
-* **Transcriptome Reference:** Bowtie2 index files
-* **Filter Reference:** Bowtie2 index files (typically for rRNA sequences)
-* **Annotation:** A bed file defining CDS, UTR5 and UTR3 regions.
-* **Transcript Lengths:** A two column tsv file containing transcript lengths
-
-2. Prepare a custom `project.yaml` file.
-You can use the sample file `project.yaml`, provided in this repository,
-as template.
-
-3. In `project.yaml`, provide RiboFlow parameters such as `clip_arguments`, alignment arguments etc.
-You can simply modify the arguments in the sample file `project.yaml` in this repository.
-
-4. You can adjust the hardware and computing environment settings in Nextflow configuration file(s).
-For Docker option, see `configs/docker_local.config`. If you are not using Docker,
-see `configs/local.config`.
-
-5. RNA-Seq data is optional for RiboFlow. So, if you do NOT have RNA-Seq data, in the project file, set
-
-`do_rnaseq: false`
-
-If you have RNA-Seq data to be paired with ribosome profiling data, see the __Advanced Features__ below.
-
-
-6. Metadata is optional for RiboFlow.. If you do NOT have metadata, in the project file, set
-
-`do_metadata: false`
-
-If you have metadata, see __Advanced Features__ below.
-
-7. Run RiboFlow using the new parameters file `project.yaml`.
-
-Using Docker:
-
-`nextflow RiboFlow.groovy -params-file project.yaml -profile docker_local`
-
-Without Docker:
-
-`nextflow RiboFlow.groovy -params-file project.yaml`
-
-## Advanced Features
-
-### RNA-Seq Data
-
-If you have RNA-Seq data that you want to pair with ribosome profiling experiments,
-provide the paths of the RNA-Seq (gzipped) fastq files in the configuration file in
-_input -> metadata_. See the file `project.yaml` in this repository for an example.
-Note that the names in defining RNA-Seq files must match the names in definig ribosome profiling data.
-Also turn set the do_rnaseq flag to true, in the project file:
-
-`do_rnaseq: true`
-
-Transcript abundance data will be stored in the output ribo file.
-
-### Metadata
-
-If you have metadata files for the ribosome profiling experiments,
-provide the paths of the metadata files (in yaml format) in the configuration file in
-_input -> metadata_. See the file `project.yaml` in this repository for an example.
-Note that the names in defining metadata files must match the names in definig ribosome profiling data.
-Also turn set the metadata flag to true, in the project file:
-
-`do_metadata: true`
-
-Metadata will be stored in the output ribo file.
-
-# nextflow pipeline
-
-This repository is a template and a library repository to help you build nextflow pipeline.
-You can fork this repository to build your own pipeline.
-To get the last commits from this repository into your fork use the following commands:
-
-```sh
-git remote add upstream gitlab_lbmc:pipelines/nextflow.git
-git pull upstream master
-```
-**If you created your `.config` file before version `0.4.0` you need to run the script `src/.update_config.sh` to use the latest docker, singularity and conda configuration (don't forget to check your config files afterward for typos).**
-
-## Getting Started
-
-These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
-
-[you can follow them here.](doc/getting_started.md)
-
-## Available tools
-
-[The list of available tools.](doc/available_tools.md)
-
-## Projects using nextflow
-
-[A list of projects using nextflow at the LBMC.](doc/nf_projects.md)
-
-## Contributing
-
-Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us.
-
-## Versioning
-
-We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tags).
-
-## Authors
-
-* **Laurent Modolo** - *Initial work*
-
-See also the list of [contributors](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/graphs/master) who participated in this project.
-
-## License
-
-This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) file for details
diff --git a/configs/docker_local.config b/configs/docker_local.config
deleted file mode 100644
index 0c597b4417485b34b5df78d9f990a9a52d220139..0000000000000000000000000000000000000000
--- a/configs/docker_local.config
+++ /dev/null
@@ -1,63 +0,0 @@
-
-// Default configuration for running the pipeline on a local machine
-
-
-process {
- // if the process name is not listed separately below
- // the following settings are used
- executor='local'
- cpus = 1
- maxRetries = 1
- errorStrategy = 'retry'
-
- cpus = 1
-
- // Override the following defaults
- // by specifying the process name
-
- withName: quality_filter{
- cpus = 4
- }
-
- withName: clip{
- cpus = 4
- }
-
- withName: filter{
- cpus = 4
- }
-
- withName: transcriptome_alignment{
- cpus = 4
- }
-
- withName: quality_filter{
- cpus = 4
- }
-
- withName: genome_alignment{
- cpus = 4
- }
-
- withName: create_ribo{
- cpus = 4
- }
-
- withName: post_genome_alignment{
- cpus = 4
- }
-
-}
-
-
-// Total number of CPUs reserved for nextflow
-executor {
- cpus = 4
-}
-
-
-docker {
- enabled = true
- runOptions = '-u $(id -u):$(id -g)'
- temp = 'auto'
-}
diff --git a/configs/local.config b/configs/local.config
deleted file mode 100644
index e16dbeafb91ddf81a5ec1f8bbfc78d3c723dcd6b..0000000000000000000000000000000000000000
--- a/configs/local.config
+++ /dev/null
@@ -1,62 +0,0 @@
-
-// Default configuration for running the pipeline on a local machine
-
-
-process {
- // if the process name is not listed separately below
- // the following settings are used
- executor='local'
- cpus = 1
- maxRetries = 1
- errorStrategy = 'retry'
-
- cpus = 1
-
- // Override the following defaults
- // by specifying the process name
-
- withName: quality_filter{
- cpus = 4
- }
-
- withName: clip{
- cpus = 4
- }
-
- withName: filter{
- cpus = 4
- }
-
- withName: transcriptome_alignment{
- cpus = 4
- }
-
- withName: quality_filter{
- cpus = 4
- }
-
- withName: genome_alignment{
- cpus = 4
- }
-
- withName: create_ribo{
- cpus = 4
- }
-
- withName: post_genome_alignment{
- cpus = 4
- }
-
-}
-
-
-// Total number of CPUs reserved for nextflow
-executor {
- cpus = 4
-}
-
-
-docker {
- enabled = false
- runOptions = '-u $(id -u):$(id -g)'
-}
diff --git a/configs/stampede_local.config b/configs/stampede_local.config
deleted file mode 100644
index 3aa1e7174a6e017ff12b98aafad43c5c90aced1a..0000000000000000000000000000000000000000
--- a/configs/stampede_local.config
+++ /dev/null
@@ -1,67 +0,0 @@
-
-// Default configuration for running the pipeline on a node of TACC Stampede2
-
-
-process {
- // if the process name is not listed separately below
- // the following settings are used
- executor='local'
- cpus = 1
- maxRetries = 1
- errorStrategy = 'retry'
-
- cpus = 1
-
-
- // Override the following defaults
- // by specifying the process name
-
- withName: md5sum {
- cpus = 1
- }
-
- withName: quality_filter{
- cpus = 4
- }
-
- withName: clip{
- cpus = 4
- }
-
- withName: filter{
- cpus = 8
- }
-
- withName: transcriptome_alignment{
- cpus = 8
- }
-
- withName: quality_filter{
- cpus = 8
- }
-
- withName: genome_alignment{
- cpus = 8
- }
-
- withName: create_ribo{
- cpus = 8
- }
-
- withName: post_genome_alignment{
- cpus = 8
- }
-
-}
-
-
-// Total number of CPUs reserved for nextflow
-executor {
- cpus = 48
-}
-
-
-docker {
- enabled = false
- runOptions = '-u $(id -u):$(id -g)'
-}
diff --git a/docker/Dockerfile b/docker/Dockerfile
deleted file mode 100644
index 711d272d1d645a5ac16df48bd3a69884829af039..0000000000000000000000000000000000000000
--- a/docker/Dockerfile
+++ /dev/null
@@ -1,31 +0,0 @@
-FROM ubuntu:18.04
-
-RUN apt-get update --fix-missing && \
- apt-get install -q -y wget curl bzip2 libbz2-dev git build-essential zlib1g-dev locales vim fontconfig ttf-dejavu
-
-
-# Set the locale
-RUN locale-gen en_US.UTF-8
-ENV LANG en_US.UTF-8
-ENV LANGUAGE en_US:en
-ENV LC_ALL en_US.UTF-8
-
-# Install conda
-RUN curl -LO http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
- bash Miniconda3-latest-Linux-x86_64.sh -p /miniconda3 -b && \
- rm Miniconda3-latest-Linux-x86_64.sh
-ENV PATH=/miniconda3/bin:${PATH}
-
-# Install conda dependencies
-ADD environment.yaml /
-ADD VERSION /
-RUN pwd
-RUN conda config --set always_yes yes --set changeps1 no && \
- conda config --add channels conda-forge && \
- conda config --add channels defaults && \
- conda config --add channels bioconda && \
- conda config --get && \
- conda update -q conda && \
- conda info -a && \
- conda env update -q -n root --file environment.yaml && \
- conda clean --tarballs --index-cache --lock
diff --git a/docker/build.sh b/docker/build.sh
deleted file mode 100644
index 180e2e5d8a09e46822bde1b36d663f944a65a87c..0000000000000000000000000000000000000000
--- a/docker/build.sh
+++ /dev/null
@@ -1,19 +0,0 @@
-set -ex
-
-cp ../VERSION ./VERSION
-cp ../environment.yaml ./environment.yaml
-
-version=$(cat ./VERSION | sed -nre 's/^[^0-9]*(([0-9]+\.)*[0-9]+).*/\1/p')
-
-function cleanup {
- rm ./VERSION
- rm ./environment.yaml
-}
-
-trap cleanup EXIT
-
-
-docker build -t ceniklab/riboflow:latest .
-docker run -it ceniklab/riboflow:latest apt list | sed 's/\x1b\[[0-9;]*m//g' > ./apt.list
-docker run -it ceniklab/riboflow:latest conda list > ./conda.list
-docker images
diff --git a/docker/deploy.sh b/docker/deploy.sh
deleted file mode 100644
index 7c416be659cc1e51afaf2925e32000f8b499de85..0000000000000000000000000000000000000000
--- a/docker/deploy.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-
-docker login -u ceniklab
-
-version=$(cat ../VERSION | sed -nre 's/^[^0-9]*(([0-9]+\.)*[0-9]+).*/\1/p')
-echo "version: $version"
-
-# push the image
-docker push ceniklab/riboflow:latest
-docker push ceniklab/riboflow:$version
diff --git a/docker/tag.sh b/docker/tag.sh
deleted file mode 100644
index c3be5db66683c25ac5dbd7b69676c673e8d57134..0000000000000000000000000000000000000000
--- a/docker/tag.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-
-set -ex
-
-version=$(cat ../VERSION | sed -nre 's/^[^0-9]*(([0-9]+\.)*[0-9]+).*/\1/p')
-echo "version: $version"
-
-# tag it
-docker tag ceniklab/riboflow:latest ceniklab/riboflow:${version}