diff --git a/.gitignore b/.gitignore
index 7ed40cac9c2a19861059c3770e7dcc8d6114624e..728cd62d4001df69740ecc6952afbb80868abc12 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,331 @@
+
+# Created by https://www.gitignore.io/api/vim,code,emacs,python,pycharm,virtualenv,sublimetext
+# Edit at https://www.gitignore.io/?templates=vim,code,emacs,python,pycharm,virtualenv,sublimetext
+
+### Code ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+
+### Emacs ###
+# -*- mode: gitignore; -*-
+*~
+\#*\#
+/.emacs.desktop
+/.emacs.desktop.lock
+*.elc
+auto-save-list
+tramp
+.\#*
+
+# Org-mode
+.org-id-locations
+*_archive
+
+# flymake-mode
+*_flymake.*
+
+# eshell files
+/eshell/history
+/eshell/lastdir
+
+# elpa packages
+/elpa/
+
+# reftex files
+*.rel
+
+# AUCTeX auto folder
+/auto/
+
+# cask packages
+.cask/
+dist/
+
+# Flycheck
+flycheck_*.el
+
+# server auth directory
+/server/
+
+# projectiles files
+.projectile
+
+# directory configuration
+.dir-locals.el
+
+# network security
+/network-security.data
+
+
+### PyCharm ###
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and WebStorm
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn. Uncomment if using
+# auto-import.
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### PyCharm Patch ###
+# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721
+
+# *.iml
+# modules.xml
+# .idea/misc.xml
+# *.ipr
+
+# Sonarlint plugin
+.idea/**/sonarlint/
+
+# SonarQube Plugin
+.idea/**/sonarIssues.xml
+
+# Markdown Navigator plugin
+.idea/**/markdown-navigator.xml
+.idea/**/markdown-navigator/
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# pyenv
+.python-version
+
+# pipenv
+# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+# However, in case of collaboration, if having platform-specific dependencies or dependencies
+# having no cross-platform support, pipenv may install dependencies that don't work, or not
+# install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+### SublimeText ###
+# Cache files for Sublime Text
+*.tmlanguage.cache
+*.tmPreferences.cache
+*.stTheme.cache
+
+# Workspace files are user-specific
+*.sublime-workspace
+
+# Project files should be checked into the repository, unless a significant
+# proportion of contributors will probably not be using Sublime Text
+# *.sublime-project
+
+# SFTP configuration file
+sftp-config.json
+
+# Package control specific files
+Package Control.last-run
+Package Control.ca-list
+Package Control.ca-bundle
+Package Control.system-ca-bundle
+Package Control.cache/
+Package Control.ca-certs/
+Package Control.merged-ca-bundle
+Package Control.user-ca-bundle
+oscrypto-ca-bundle.crt
+bh_unicode_properties.cache
+
+# Sublime-github package stores a github token in this file
+# https://packagecontrol.io/packages/sublime-github
+GitHub.sublime-settings
+
+### Vim ###
+# Swap
+[._]*.s[a-v][a-z]
+[._]*.sw[a-p]
+[._]s[a-rt-v][a-z]
+[._]ss[a-gi-z]
+[._]sw[a-p]
+
+# Session
+Session.vim
+Sessionx.vim
+
+# Temporary
+.netrwhist
+
+# Auto-generated tag files
+tags
+
+# Persistent undo
+[._]*.un~
+
+# Coc configuration directory
+.vim
+
+### VirtualEnv ###
+# Virtualenv
+# http://iamzed.com/2009/05/07/a-primer-on-virtualenv/
+pyvenv.cfg
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+pip-selfcheck.json
+
+# End of https://www.gitignore.io/api/vim,code,emacs,python,pycharm,virtualenv,sublimetext
+
+# Custom additions
+.vscode
.DS_Store
snakemake/.*
-snakemake/logs
-snakemake/results/
+runs/.*
+!runs/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 43321795ef74fd293cab88baace30000bec42220..b352d59535beb2db9493226c18d13709a6104da3 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,7 +1,7 @@
image: snakemake/snakemake:v5.9.1
before_script:
- - pip install biopython==1.76
+ - pip install -r scripts/requirements.txt
test:
script:
diff --git a/README.md b/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..5c5cdb4db3b25b2dde318caf904db4f50351a2cc
--- /dev/null
+++ b/README.md
@@ -0,0 +1,298 @@
+# RNA-Seq pipeline
+
+[Snakemake] workflow for general purpose RNA-Seq library annotation developed
+by the [Zavolan lab].
+
+Reads are processed, aligned, quantified and analyzed with state-of-the-art
+tools to give meaningful initial insights into various aspects of an RNA-Seq
+library while cutting down on hands-on time for bioinformaticians.
+
+The scheme below is a visual representation of an example run of the
+workflow:
+
+> 
+
+## Installation
+
+### Installing Singularity
+
+For improved reproducibility and reusability of the workflow, as well as an
+easy means to run it on a high performance computing (HPC) cluster managed,
+e.g., by [Slurm], each individual step of the workflow runs in its own
+container. Specifically, containers are created out of [Singularity] images
+built for each software used within the workflow. As a consequence, running
+this workflow has very few individual dependencies. It does, however, require
+that Singularity be installed. See the links below for installation
+instructions for the most up-to-date (as of writing) as well as for the tested
+version (2.6.1) of Singularity:
+
+- [Singularity v3.5](https://sylabs.io/guides/3.5/user-guide/quick_start.html)
+- [Singularity v2.6](https://sylabs.io/guides/2.6/user-guide/installation.html)
+
+### Setting up a Snakemake virtual environment
+
+In addition to Singularity, [Snakemake] needs to be installed. We strongly
+recommended to do so via a virtual environment. Here we describe the steps
+necessary to set up such a virtual environment with a recent version (v4.4+) of
+the `conda` package manager. If you prefer to use another solution, such as
+`virtualenv`, adapt the steps according to the specific instructions of your
+preferred solution.
+
+If you do not have `conda` installed for Python3, we recommend to install the
+minimal version (Python and package manager) [Miniconda] (see the link for
+installation instructions). Be sure to select the correct version for your
+operating system and ensure that you select the Python 3 option.
+
+To create and activate the environment, run:
+
+```bash
+conda create -n rnaseq_pipeline \
+ -c bioconda \
+ -c conda-forge \
+ snakemake=5.10.0
+conda activate rnaseq_pipeline
+```
+
+### Cloning the repository
+
+Traverse to the desired path on your file system, then clone the repository and
+move into it with:
+
+```bash
+git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/rnaseqpipeline.git
+cd rnaseqpipeline
+```
+
+All installation requirements should now be met with.
+
+## Testing the installation
+
+We have prepared several tests to check the integrity of the workflow. The
+most important one lets you execute the workflow on a small set of example
+input files.
+
+### Run workflow on local machine
+
+Execute the following command to run the test workflow on your local machine:
+
+```bash
+bash tests/test_integration_workflow/test.local.sh
+```
+
+### Run workflow via Slurm
+
+Execute the following command to run the test workflow on a Slurm-managed HPC.
+
+```bash
+bash tests/test_integration_workflow/test.local.sh
+```
+
+> **NOTE:** Depending on the configuration of your Slurm installation or if
+> using a different workflow manager, you may need to adapt file `cluster.json`
+> and the arguments to options `--config` and `--cores` in file
+> `test.slurm.sh`, both located in directory `tests/test_integration_workflow`.
+> Consult the manual of your workload manager as well as the section of the
+> Snakemake manual dealing with [cluster execution].
+
+## Running the workflow on your own samples
+
+1. Assuming that you are currently inside the repository's root directory,
+create a directory for your workflow run and traverse inside it with:
+
+ ```bash
+ mkdir runs/my_run
+ cd runs/my_run
+ ```
+
+2. Create empty sample table, workflow configuration and, if necessary, cluster
+configuration files:
+
+ ```bash
+ touch samples.tsv
+ touch config.yaml
+ touch cluster.json
+ ```
+
+3. Use your editor of choice to manually populate these files with appropriate
+values. Have a look at the examples in the `tests/` directory to see what the
+files should look like, specifically:
+
+ - [samples.tsv](tests/test_integration_workflow/input_files/samples.tsv)
+ - [config.yaml](tests/test_integration_workflow/config.yaml)
+ - [cluster.json](tests/test_integration_workflow/cluster.json)
+
+4. Create a runner script. Pick one of the following choices for either local
+or cluster execution. Before execution of the respective command, you must
+replace the data directory placeholders in the argument to the
+`--singularity-args` option with a comma-separated list of _all_ directories
+containing input data files (samples and any annoation files etc) required for
+your run.
+
+ Runner script for _local execution_:
+
+ ```bash
+ cat << "EOF" > run.sh
+ #!/bin/bash
+ mkdir -p logs/local_log
+ snakemake \
+ --snakefile="../../snakemake/Snakefile" \
+ --configfile="config.yaml" \
+ --cores=4 \
+ --printshellcmds \
+ --rerun-incomplete \
+ --use-singularity \
+ --singularity-args="--bind <data_dir_1>,<data_dir_2>,<data_dir_n>"
+ EOF
+ ```
+
+ **OR**
+
+ Runner script for _Slurm cluster exection_ (note that you may need
+ to modify the arguments to `--cluster` and `--cores` depending on your HPC
+ and workload manager configuration):
+
+ ```bash
+ cat << "EOF" > run.sh
+ #!/bin/bash
+ mkdir -p logs/cluster_log
+ snakemake \
+ --snakefile="../../snakemake/Snakefile" \
+ --configfile="config.yaml" \
+ --cluster-config="cluster.json" \
+ --cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
+ --cores=256 \
+ --printshellcmds \
+ --rerun-incomplete \
+ --use-singularity \
+ --singularity-args="--bind <data_dir_1>,<data_dir_2>,<data_dir_n>"
+ EOF
+ ```
+
+5. Start your workflow run:
+
+ ```bash
+ bash run.sh
+ ```
+
+### Configuring workflow runs via LabKey tables
+
+Our lab stores metadata for sequencing samples in a locally deployed [LabKey]
+instance. This repository provides two scripts that give programmatic access to
+the LabKey data table and convert it to the corresponding workflow inputs
+(`samples.tsv` and `config.yaml`), respectively. As such, these scripts largely
+automate step 3. of the above instructions. However, as these scripts were
+specifically for the needs of our lab, they are likely not portable or, at
+least, will require considerable modification for other setups (e.g., different
+LabKey table structure).
+
+> **NOTE:** All of the below steps assume that your current working directory
+> is the repository's root directory.
+
+1. The scripts have additional dependencies that can be installed with:
+
+ ```bash
+ pip install -r scripts/requirements.txt
+ ```
+
+2. In order to gain programmatic access to LabKey via its API, a credential
+file is required. Create it with the following command after replacing the
+placeholder values with your real credentials (talk to your LabKey manager if
+you do not have these):
+
+ ```bash
+ cat << EOF | ( umask 0377; cat >> ${HOME}/.netrc; )
+ machine <remote-instance-of-labkey-server>
+ login <user-email>
+ password <user-password>
+ EOF
+ ```
+
+3. Run the LabKey API client script:
+
+ ```bash
+ python scripts/labkey_api.py <project_name> <labkey_table_nane>
+ ```
+
+ > **NOTE:** Right now the script only prints a `pandas` data frame
+ > representation of the LabKey table on the screen and manually needs to be
+ > saved to a file for the next step. Ultimately the script will produce
+ > either a file in table format or will be merged with the following
+ > script.
+
+4. Generate the workflow configuration with the following command, after
+replacing the placeholders with the appropriate values:
+
+ ```bash
+ python scripts scripts/labkey_to_snakemake.py \
+ --input_table=<labkey_output_table> \
+ --input_dict="scripts/input_dict.tsv" \
+ --config_file="runs/my_run/config.yaml" \
+ --samples_table="runs/my_run/samples.tsv" \
+ --genomes_path=<path_to_annotation_files>
+ ```
+
+#### Additional information
+
+The metadata field names in the LabKey instance and those in the parameters
+in the Snakemake workflow have different names. A mapping between LabKey
+field identifiers and Snakemake parameters is listed below:
+
+Labkey | Snakemake
+--- | ---
+Entry date | entry_date
+Path to FASTQ file(s) | fastq_path
+Condition name | condition
+Replicate name | replicate_name
+End type (PAIRED or SINGLE) | seqmode
+Name of Mate1 FASTQ file | fq1
+Name of Mate2 FASTQ file | fq2
+Direction of Mate1 (SENSE, ANTISENSE or RANDOM) | mate1_direction
+Direction of Mate2 (SENSE, ANTISENSE or RANDOM) | mate2_direction
+5' adapter of Mate1 | fq1_5p
+3' adapter of Mate1 | fq1_3p
+5' adapter of Mate2 | fq2_5p
+3' adapter of Mate2 | fq2_3p
+Fragment length mean | mean
+Fragment length SD | sd
+Quality control flag (PASSED or FAILED) | quality_control_flag
+Checksum of raw Mate1 FASTQ file | mate1_checksum
+Checksum of raw Mate2 FASTQ file | mate2_checksum
+Name of metadata file | metadata
+Name of quality control file for Mate1 | mate1_quality
+Name of quality control file for Mate2 | mate2_quality
+Organism | organism
+Taxon ID | taxon_id
+Name of Strain / Isolate / Breed / Ecotype | strain_name
+Strain / Isolate / Breed / Ecotype ID | strain_id
+Biomaterial provider | biomaterial_provider
+Source / tissue name | source_name
+Tissue code | tissue_code
+Additional tissue description | tissue_description
+Genotype short name | genotype_name
+Genotype description | genotype_description
+Disease short name | disease_name
+Disease description | disease_description
+Abbreviation for treatment | treatment
+Treatment description | treatment_description
+Gender | gender
+Age | age
+Developmental stage | development_stage
+Passage number | passage_number
+Sample preparation date (YYYY-MM-DD) | sample_prep_date
+Prepared by | prepared_by
+Documentation | documentation
+Name of protocol file | protocol_file
+Sequencing date (YYYY-MM-DD) | seq_date
+Sequencing instrument | seq_instrument
+Library preparation kit | library_kit
+Cycles | cycles
+Molecule | molecule
+Contaminant sequences | contaminant_seqs
+
+[cluster execution]: <https://snakemake.readthedocs.io/en/stable/executing/cluster-cloud.html#cluster-execution>
+[LabKey]: <https://www.labkey.com/>
+[Miniconda]: <https://docs.conda.io/en/latest/miniconda.html>
+[Snakemake]: <https://snakemake.readthedocs.io/en/stable/>
+[Singularity]: <https://sylabs.io/singularity/>
+[Slurm]: <https://slurm.schedmd.com/documentation.html>
+[Zavolan lab]: <https://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/zavolan/research-group-mihaela-zavolan/>
diff --git a/runs/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE b/runs/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/tests/test_scripts_labkey_to_snakemake/input_dict.tsv b/scripts/input_dict.tsv
similarity index 100%
rename from tests/test_scripts_labkey_to_snakemake/input_dict.tsv
rename to scripts/input_dict.tsv
diff --git a/scripts/requirements.txt b/scripts/requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba30bb94d58fb884542c3bdaeba006058ba7fe3e
--- /dev/null
+++ b/scripts/requirements.txt
@@ -0,0 +1,3 @@
+biopython==1.76
+labkey==1.2.0
+pandas==0.25.3
diff --git a/tests/test_create_dag_chart/config.yaml b/tests/test_create_dag_chart/config.yaml
index dade873fec556edaf954f8cb72d7d4b39097eb81..e1d111b8e0a7f835e0600c476417dd1ce779a9d6 100644
--- a/tests/test_create_dag_chart/config.yaml
+++ b/tests/test_create_dag_chart/config.yaml
@@ -25,5 +25,5 @@
##############################################################################
### Sample info
##############################################################################
- samples: "input_files/samples.tsv"
+ samples: "samples.tsv"
...
diff --git a/tests/test_create_dag_chart/input_files/samples.tsv b/tests/test_create_dag_chart/samples.tsv
similarity index 100%
rename from tests/test_create_dag_chart/input_files/samples.tsv
rename to tests/test_create_dag_chart/samples.tsv
diff --git a/tests/test_integration_workflow/config.yaml b/tests/test_integration_workflow/config.yaml
index dade873fec556edaf954f8cb72d7d4b39097eb81..e1d111b8e0a7f835e0600c476417dd1ce779a9d6 100644
--- a/tests/test_integration_workflow/config.yaml
+++ b/tests/test_integration_workflow/config.yaml
@@ -25,5 +25,5 @@
##############################################################################
### Sample info
##############################################################################
- samples: "input_files/samples.tsv"
+ samples: "samples.tsv"
...
diff --git a/tests/test_integration_workflow/input_files/samples.tsv b/tests/test_integration_workflow/samples.tsv
similarity index 100%
rename from tests/test_integration_workflow/input_files/samples.tsv
rename to tests/test_integration_workflow/samples.tsv
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
index 926b70c0caaa9ce015c2cfb06838c25a5feef7d5..f01c00b36dd78366d01cd068a7038b723aa64139 100755
--- a/tests/test_integration_workflow/test.local.sh
+++ b/tests/test_integration_workflow/test.local.sh
@@ -20,7 +20,7 @@ snakemake \
--printshellcmds \
--rerun-incomplete \
--use-singularity \
- --singularity-args "--bind ${PWD}"
+ --singularity-args="--bind ${PWD}"
find results/ -type f -name \*\.gz -exec gunzip '{}' \;
md5sum --check "expected_output.md5"
diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
index 719d1fd7bc7fe8afcad5decdc36e2815cfc2b03e..ad278d9d2580acd7421f86f8bed5389186457419 100755
--- a/tests/test_integration_workflow/test.slurm.sh
+++ b/tests/test_integration_workflow/test.slurm.sh
@@ -23,7 +23,7 @@ snakemake \
--printshellcmds \
--rerun-incomplete \
--use-singularity \
- --singularity-args "--bind ${PWD}"
+ --singularity-args="--bind ${PWD}"
find results/ -type f -name \*\.gz -exec gunzip '{}' \;
md5sum --check "expected_output.md5"
diff --git a/tests/test_scripts_labkey_to_snakemake/test.sh b/tests/test_scripts_labkey_to_snakemake/test.sh
index 06c50ccc165d2c3ab3402ca1e00645cf7499bd5f..68d740d6993586142ec3d25e68e2be5245e89029 100755
--- a/tests/test_scripts_labkey_to_snakemake/test.sh
+++ b/tests/test_scripts_labkey_to_snakemake/test.sh
@@ -14,7 +14,7 @@ cd $script_dir
# Run tests
python "../../scripts/labkey_to_snakemake.py" \
--input_table="input_table.tsv" \
- --input_dict="input_dict.tsv" \
+ --input_dict="../../scripts/input_dict.tsv" \
--config_file="config.yaml" \
--samples_table="samples.tsv" \
--genomes_path="."