update metadata to v1.1.0

Author: ptrebert

.editorconfig

@@ -6,13 +6,14 @@ root = true
 [*]
 end_of_line = lf
 insert_final_newline = true
+trim_trailing_whitespace = true
 charset = utf-8
 indent_style = space
 indent_size = 4
 
 [*.{tsv,tab}]
 indent_style = tab
 
-[*.{yml,yaml,json}]
+[*.{yml,yaml,json,toml,tml}]
 indent_style = space
 indent_size = 2

.gitignore

@@ -1,3 +1,63 @@
+# ====================
+# gitignore entries
+# for R
+# ====================
+
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.RDataTmp
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/
+
+# ====================
+# gitignore entries
+# for PYTHON
+# ====================
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -128,6 +188,11 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+# ====================
+# gitignore entries
+# CUSTOM
+# ====================
+
 # VS code
 .vscode/
 

CITATION.md

@@ -0,0 +1,69 @@
+# Citing this repository
+
+If you are using the content of this repository in whole or in part for your own work,
+please credit the Core Unit Bioinformatics in an appropriate form.
+
+In general, please add this statement to the acknowledgments of your publication:
+
+    This work was supported by the Core Unit Bioinformatics
+    of the Medical Faculty of the Heinrich Heine University Düsseldorf.
+
+Additionally, please follow the below instructions to obtain a citable reference
+for your publication.
+
+## Identifying the right source link
+
+Each repository of the Core Unit Bioinformatics is assigned a persistent
+identifier (PID) at some point (usually after the prototype stage). Please use
+this PID to link to the repository. You always find the PID in the top-level
+`pyproject.toml`. Depending on the type of repository (project, workflow, or
+workflow template), the relevant PID is listed in the corresponding metadata
+section:
+
+```toml
+# workflow repository
+[cubi.workflow]
+pid = "THE-PID"
+```
+
+```toml
+# workflow template repository
+[cubi.workflow.template]
+pid = "THE-PID"
+```
+
+```toml
+# project repository
+[cubi.project]
+pid = "THE-PID"
+```
+
+If a PID has not yet been assigned to the repository, please use the repository URL,
+and, if time permits, contact the repository maintainer regarding assigning a PID
+in the near future.
+
+### 1. Release version
+
+For release versions, please use the respective version string in addition to the source link,
+i.e. ideally in combination with the PID, and integrate that information into your list
+of references as appropriate.
+
+Note that repositories of the type "project" may not contain a lot of code, and are thus
+often not amenable to the usual "release cycle" following bug fixes, feature integrations and so on.
+Hence, the "project" metadata do not contain a "version" key (as opposed to workflow and workflow
+template repositories). See the next point if you encounter that situation.
+
+### 2. Development (non-release) version
+
+For development versions, please use the respective git commit hash in addtion to the source link,
+i.e. ideally in combination with the PID, and integrate that information into your list
+of references as appropriate. It is strongly recommended to only use git commits from the two
+central branches `main` and `dev`.
+
+If a "project" repository is lacking an explicit release version, please use the same strategy
+to obtain a citable reference of the repository.
+
+
+### 3. None of the above
+
+Please get in touch and we'll find a solution for your case :-)

README.md

@@ -26,19 +26,4 @@ Add info here - be concise, and provide more details in [the workflow documentat
 
 # Citation
 
-If you use this workflow (or non-trivial parts of it such as a whole sub-module),
-please credit the Core Unit Bioinformatics as follows:
-
-1. you use a release version with DOI:
-    - please use the DOI to link to the workflow version
-    - integrate the DOI into the references of your publication (if applicable)
-2. you use a dev/non-release version:
-    - please link to the workflow repository where appropriate (e.g., in your Methods section)
-    - (recommended: report the exact commit hash you are referring to)
-    - please add the following statement to your acknowledgements:
-    ```
-    This work was supported by the Core Unit Bioinformatics of the Medical Faculty
-    of the Heinrich Heine University Düsseldorf.
-    ```
-3. you think none of the above options apply in your case:
-    - please get in touch and let's talk about it :-)
+If not indicated otherwise above, please follow [these instructions](CITATION.md) to cite this repository in your own work.

pyproject.toml

@@ -1,5 +1,3 @@
-
-
 [tool.black]
 line-length = 88
 
@@ -16,17 +14,22 @@ disable=[
 [tool.isort]
 profile = "black"
 
-[cubi.project]
+[cubi.metadata]
 pid = "undefined"
-name = "undefined"
-date = 2000-01-01
+version = "1.1.0"
 
-[cubi.workflow]
-pid = "undefined"
-name = "undefined"
-version = "prototype"
+[cubi.metadata.naming.workflow.system]
+smk="snakemake"
+nxf="nextflow"
+cwl="common-workflow-language"
+wdl="workflow-definition-language"
+
+[cubi.metadata.naming.project.type]
+dev="development"
+run="production-run"
+bmk="benchmark"
 
 [cubi.workflow.template]
 pid = "undefined"
-system = "snakemake"
+system = "smk"
 version = "prototype"

workflow/envs/dev_env.yaml

@@ -12,6 +12,7 @@ dependencies:
   - numpy=1.23.1
   - pyyaml=6.0
   - toml=0.10.2
+  - semver=2.13.0
   - coincbc=2.10.8
   - pylint=2.14.5
   - isort=5.10.1

workflow/envs/exec_env.yaml

@@ -12,4 +12,5 @@ dependencies:
   - numpy=1.23.1
   - pyyaml=6.0
   - toml=0.10.2
+  - semver=2.13.0
   - coincbc=2.10.8