Add support for Nextflow version 22.03.0-edge and later (#43)

* Set DSL1 in nextflow code
* Update usage/installation docs about Nextflow DSL2
* Update _version.py to v1.1.3
* Hide html doc dir in gitignore

.gitignore

@@ -1,3 +1,4 @@
 __pycache__
 .vscode
 .nextflow
+doc/source/html

doc/source/installation.rst

@@ -16,9 +16,12 @@ To install `Nextflow <https://www.nextflow.io>`__ and its dependencies, follow t
 
 *   Make sure you have Bash 3.2 (or later) installed.
 
-*   If you do not have `Java <https://www.oracle.com/java/>`__ installed, install `Java 8 (or later, up to 15) <https://www.oracle.com/java/technologies/javase-downloads.html>`__; on Linux you can for example use::
+*   If you do not have `Java <https://www.oracle.com/java/>`__ installed, install `Java 11 or later <https://www.oracle.com/java/technologies/javase-downloads.html>`__; on Linux you can for example use::
 
-        sudo apt-get install default-jdk
+        sudo apt-get install default-jdk  
+   
+   .. note::
+      Nextflow versions before ``22.01.x-edge`` `require <https://www.nextflow.io/blog/2022/evolution-of-nextflow-runtime.html>`__ Java version 8 up to 15 for their execution.
 
 *   Then install Nextflow using either::
 
@@ -31,6 +34,9 @@ To install `Nextflow <https://www.nextflow.io>`__ and its dependencies, follow t
 
     This creates the ``nextflow`` executable file in the current directory.
 
+.. note::
+   `ksrates`'s Nextflow pipeline is written using the older DSL1 syntax, which will be `removed <https://www.nextflow.io/blog/2022/evolution-of-nextflow-runtime.html>`__ after Nextflow version ``22.10.x`` in favor of DSL2. Using Nextflow version ``22.03.0-edge`` or later will require the use of `ksrates` version ``v1.1.3`` or later. We will do our best to preserve compatibility with future Nextflow versions.
+
 *   Optionally make the ``nextflow`` executable accessible by your ``$PATH`` variable, for example by moving it::
 
         sudo mv nextflow /usr/local/bin 

doc/source/usage.rst

@@ -36,6 +36,11 @@ The *ksrates* pipeline can be automatically run through Nextflow with a few prep
 
         nextflow run VIB-PSB/ksrates --config ./config_elaeis.txt
 
+    .. note::
+       Please update `ksrates` to version ``v1.1.3`` or later when launching it with Nextflow versions ``22.03.0-edge`` or later to prevent compatibility issues. See our :ref:`installation page <install_nextflow>` about how to get the latest Nextflow version. You can also launch a specific (e.g. previous) Nextflow version through the ``NXF_VER`` environmental `variable <https://www.nextflow.io/docs/latest/getstarted.html#updates>`__ in the command line::
+
+            NXF_VER=21.10.6 nextflow run VIB-PSB/ksrates --config ./config_elaeis.txt
+    
     The *ksrates configuration file* is specified through the ``--config`` parameter. The *Nextflow configuration file* is automatically recognized when it's named with the Nextflow-reserved ``nextflow.config`` file name and located in the launching directory; alternatively, the user can provide a custom file by specifying its name or path using the ``-C`` option (see `Nextflow documentation <https://www.nextflow.io/docs/latest/cli.html#hard-configuration-override>`__).
     
     The first time the command is launched it downloads the *ksrates* Nextflow pipeline from the ``VIB-PSB/ksrates`` GitHub repository; from then on it uses the local copy stored in the ``$HOME/.nextflow`` directory. If running a container, the image is pulled from Docker Hub and stored locally for successive usage. The Singularity container is stored by default in the launching folder under ``work/singularity``.

ksrates/_version.py

@@ -1 +1 @@
-__version__ = "1.1.1"
+__version__ = "1.1.3"

main.nf

@@ -1,4 +1,5 @@
 #!/usr/bin/env nextflow
+nextflow.enable.dsl = 1
 
 // should probably use our own Logger...
 LOG_OUTPUT = true  // log process and other output via log.info