Created skeleton for data analysis projects.

cookiecutter.json

+{
+    "full_name": "Jeroen F.J. Laros",
+    "email": "J.F.J.Laros@lumc.nl",
+    "client_full_name": "John Doe",
+    "client_email": "J.Doe@lumc.nl",
+    "sequencing_centre": "LGTC",
+    "sequencing_platform": "Illumina HiSeq 2500",
+    "molecular_type": "RNA",
+    "experiment_type": "RNASeq",
+    "project_name": "jdoe-rnaseq"
+}

{{cookiecutter.project_name}}/README.md

+# General information
+{{ cookiecutter.experiment_type }} data analysis for {{ cookiecutter.client_full_name }}.
+
+## Contact information
+Owner: {{ cookiecutter.client_full_name }} <{{ cookiecutter.client_email }}>
+Project leader: {{ cookiecutter.full_name }} <{{ cookiecutter.email }}>
+
+## Hours spent
+{{ cookiecutter.full_name }}: 1
+

{{cookiecutter.project_name}}/analysis/README.md

+# Data analysis
+Here we describe all data analyses done for this project. Every analysis is in
+a separate folder.
+
+## Analyses
+`folder_name`: Short description.
+

{{cookiecutter.project_name}}/data/README.md

+# Data
+Here we store all raw data (i.e., delivered by the client or from the
+sequencing centre). Also see *Notes* below.
+
+## Details
+Sequencing centre: {{ cookiecutter.sequencing_centre }}
+Platform: {{ cookiecutter.sequencing_platform }}
+Molecular type: {{ cookiecutter.molecular_type }}
+Experiment type:  {{ cookiecutter.experiment_type }}
+Owner: {{ cookiecutter.client_full_name }} <{{ cookiecutter.client_email }}>
+Data gathered by: {{ cookiecutter.full_name }} <{{ cookiecutter.email }}>
+
+## Notes
+Since storage on our GitLab server and desktop computers is limited, it is not
+a good idea to track very large files directly in the repository. However, we
+do want to have some way to track our input and output data (which is usually
+quite large). A solution for this is provided by
+[Git-annex](http://git-annex.branchable.com/).
+
+Git-annex allows you to manage large files with git without storing their
+contents in git. It works by storing file checksums in git instead of their
+contents.
+
+To track a large file using Git-annex, use `git annex add <filename>`. You can
+now do `git commit` as normal.
+
+For more information, please see the
+[Git-annex walkthrough](http://git-annex.branchable.com/walkthrough/).
+

{{cookiecutter.project_name}}/doc/README.md

+# User supplied documentation
+Documentation on the project, such as annotated sample lists, the goal of the
+project, related work and literature.
+
+## Files
+`filename`: Short description.
+

{{cookiecutter.project_name}}/src/README.md

+# Custom software
+Any custom scripts and specific software versions for this project are stored
+here. Please consider moving things to their own repository when you think they
+might be useful for other projects as well.
+
+## Software
+`name`: Short description.
+