diff --git a/kubernetes/Dockerfile b/cwl/Dockerfile
similarity index 96%
rename from kubernetes/Dockerfile
rename to cwl/Dockerfile
index 0a3e1a95be118cb5a5b90f0f7d0ad6124bb00b9c..95b351aa625d8d4ac46f037d690fe44319df6336 100644
--- a/kubernetes/Dockerfile
+++ b/cwl/Dockerfile
@@ -26,7 +26,7 @@ ENV DEBIAN_FRONTEND=noninteractive LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LANGUAGE=en_U
RUN apt-get update && apt-get install --yes build-essential cpanminus curl git gnupg htop libfontconfig1 locales nano nodejs pigz python3-dev python3-distutils python3.8 raptor2-utils raptor2-utils sshpass unzip wget zip libblas-dev liblapack-dev zlib1g-dev pkg-config libhdf5-100 libhdf5-dev gfortran libblas-dev liblapack-dev zlib1g-dev pkg-config libhdf5-100 libhdf5-dev gfortran libbz2-dev python-setuptools libidn11 rsync
RUN curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && python3.8 get-pip.py && \
- python3.8 -m pip install cwltool==3.1.20220224085855 &&\
+ python3.8 -m pip install git+https://github.com/common-workflow-language/cwltool.git@empty_scatter_fix &&\
cwltool --version && python3.8 -m pip install html5lib
# Enable icommands
@@ -96,6 +96,9 @@ ENV PATH=$PATH:$SDKMAN:$CHECKM:$GTDBTK:$CONDA
######################################
######################################
+# Add setup folder for CWL dependencies
+RUN git clone https://gitlab.com/m-unlock/cwl /setup
+
# Add anonymous access
COPY irods /root/.irods
diff --git a/kubernetes/build.sh b/cwl/build.sh
similarity index 78%
rename from kubernetes/build.sh
rename to cwl/build.sh
index 342602edcaab0dd8432d71816640a49a199387cb..2c5e8240e9e2a538a7e2379bdce13cb213fa2fce 100755
--- a/kubernetes/build.sh
+++ b/cwl/build.sh
@@ -17,8 +17,8 @@ git -C $DIR pull
# Build the docker file
#============================================================================
-docker pull docker-registry.wur.nl/unlock/docker:kubernetes
+docker pull docker-registry.wur.nl/unlock/docker:cwl
-docker build -t docker-registry.wur.nl/unlock/docker:kubernetes .
+docker build -t docker-registry.wur.nl/unlock/docker:cwl .
-docker push docker-registry.wur.nl/unlock/docker:kubernetes
\ No newline at end of file
+docker push docker-registry.wur.nl/unlock/docker:cwl
\ No newline at end of file
diff --git a/kubernetes/conda/picrust2_env.yml b/cwl/conda/picrust2_env.yml
similarity index 100%
rename from kubernetes/conda/picrust2_env.yml
rename to cwl/conda/picrust2_env.yml
diff --git a/kubernetes/docker-compose/docker-compose.yml b/cwl/docker-compose/docker-compose.yml
similarity index 100%
rename from kubernetes/docker-compose/docker-compose.yml
rename to cwl/docker-compose/docker-compose.yml
diff --git a/kubernetes/docker-compose/irods/Dockerfile b/cwl/docker-compose/irods/Dockerfile
similarity index 100%
rename from kubernetes/docker-compose/irods/Dockerfile
rename to cwl/docker-compose/irods/Dockerfile
diff --git a/kubernetes/docker-compose/rancher/Dockerfile b/cwl/docker-compose/rancher/Dockerfile
similarity index 100%
rename from kubernetes/docker-compose/rancher/Dockerfile
rename to cwl/docker-compose/rancher/Dockerfile
diff --git a/kubernetes/files/user-settings.mkfg b/cwl/files/user-settings.mkfg
similarity index 100%
rename from kubernetes/files/user-settings.mkfg
rename to cwl/files/user-settings.mkfg
diff --git a/kubernetes/gitconfig b/cwl/gitconfig
similarity index 100%
rename from kubernetes/gitconfig
rename to cwl/gitconfig
diff --git a/kubernetes/gitlab-admin-service-account.yaml b/cwl/gitlab-admin-service-account.yaml
similarity index 100%
rename from kubernetes/gitlab-admin-service-account.yaml
rename to cwl/gitlab-admin-service-account.yaml
diff --git a/kubernetes/irods/.gitkeep b/cwl/irods/.gitkeep
similarity index 100%
rename from kubernetes/irods/.gitkeep
rename to cwl/irods/.gitkeep
diff --git a/kubernetes/irods/irods_environment.json b/cwl/irods/irods_environment.json
similarity index 100%
rename from kubernetes/irods/irods_environment.json
rename to cwl/irods/irods_environment.json
diff --git a/kubernetes/kube_instance/deploy.sh b/cwl/kube_instance/deploy.sh
similarity index 100%
rename from kubernetes/kube_instance/deploy.sh
rename to cwl/kube_instance/deploy.sh
diff --git a/cwl/kube_instance/nodes.txt b/cwl/kube_instance/nodes.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b7eed42293c89f0423b86ebb1de83503e4992d1
--- /dev/null
+++ b/cwl/kube_instance/nodes.txt
@@ -0,0 +1 @@
+nibi
diff --git a/cwl/kube_instance/template_instance.yaml b/cwl/kube_instance/template_instance.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..62fe2c714855a89a0d23da1d3d541074ff8878d8
--- /dev/null
+++ b/cwl/kube_instance/template_instance.yaml
@@ -0,0 +1,80 @@
+apiVersion: v1
+kind: Pod
+metadata:
+ name: munlock-instance-HOSTNAME
+ namespace: unlock
+ labels:
+ purpose: live-instance
+spec:
+ containers:
+ - name: munlock-instance-HOSTNAME
+ image: docker-registry.wur.nl/unlock/docker:kubernetes
+ # Just spin & wait forever
+ command: [ "/bin/sh", "-c", "--" ]
+ args: [ "apt-get install -y screen; while true; do sleep 30; done;" ]
+ envFrom:
+ - configMapRef:
+ name: path
+ env:
+ - name: irodsHost
+ valueFrom:
+ secretKeyRef:
+ name: unlock-secret
+ key: irodsHost
+ - name: irodsPort
+ valueFrom:
+ secretKeyRef:
+ name: unlock-secret
+ key: irodsPort
+ - name: irodsUserName
+ valueFrom:
+ secretKeyRef:
+ name: unlock-secret
+ key: irodsUserName
+ - name: irodsZone
+ valueFrom:
+ secretKeyRef:
+ name: unlock-secret
+ key: irodsZone
+ - name: irodsAuthScheme
+ valueFrom:
+ secretKeyRef:
+ name: unlock-secret
+ key: irodsAuthScheme
+ - name: irodsHome
+ valueFrom:
+ secretKeyRef:
+ name: unlock-secret
+ key: irodsHome
+ - name: irodsCwd
+ valueFrom:
+ secretKeyRef:
+ name: unlock-secret
+ key: irodsCwd
+ - name: irodsPassword
+ valueFrom:
+ secretKeyRef:
+ name: unlock-secret
+ key: irodsPassword
+ - name: irodsSSL
+ valueFrom:
+ secretKeyRef:
+ name: unlock-secret
+ key: irodsSSL
+ resources:
+ limits:
+ cpu: '10'
+ memory: 10000Mi
+ requests:
+ cpu: '10'
+ memory: 10000Mi
+ volumeMounts:
+ - mountPath: /unlock
+ name: unlock
+ restartPolicy: OnFailure
+ volumes:
+ - name: unlock
+ persistentVolumeClaim:
+ claimName: unlock
+ nodeSelector:
+ kubernetes.io/hostname: HOSTNAME
\ No newline at end of file
diff --git a/kubernetes/run.sh b/cwl/run.sh
similarity index 100%
rename from kubernetes/run.sh
rename to cwl/run.sh
diff --git a/kubernetes/scripts/Renviron b/cwl/scripts/Renviron
similarity index 100%
rename from kubernetes/scripts/Renviron
rename to cwl/scripts/Renviron
diff --git a/kubernetes/scripts/clustalo.py b/cwl/scripts/clustalo.py
similarity index 100%
rename from kubernetes/scripts/clustalo.py
rename to cwl/scripts/clustalo.py
diff --git a/kubernetes/scripts/connect.py b/cwl/scripts/connect.py
similarity index 100%
rename from kubernetes/scripts/connect.py
rename to cwl/scripts/connect.py
diff --git a/cwl/scripts/deploy.sh b/cwl/scripts/deploy.sh
new file mode 100755
index 0000000000000000000000000000000000000000..908940ba84fe643a696d0d03abbb576d5b435801
--- /dev/null
+++ b/cwl/scripts/deploy.sh
@@ -0,0 +1,46 @@
+#!/bin/bash
+#==========================================================================================
+#title :Unlock docs deploy
+#description :Deploy script by copying CWL files to the corresponding iRODS webdav folder
+#author :Bart Nijsse & Jasper Koehorst
+#date :2021
+#version :0.0.2
+#==========================================================================================
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+# Perform a git pull
+cd $DIR && git pull
+
+if [ $? -ne 0 ]; then
+ echo "Git pull error"
+ exit $?
+fi
+
+
+###################################
+# Mac volume mount location
+DIRECTORY=/Volumes/unlock-icat.irods.surfsara.nl/infrastructure/binaries/scripts/
+
+if [ -d "$DIRECTORY" ]; then
+ echo "Copying files to "$DIRECTORY
+ rsync -vah --size-only $DIR/ $DIRECTORY/ --delete
+fi
+
+###################################
+# Other mount locations
+DIRECTORY=/run/user/1000/gvfs/dav:host=unlock-icat.irods.surfsara.nl,ssl=true/infrastructure/binaries/scripts/
+
+if [ -d "$DIRECTORY" ]; then
+ echo "Copying files to "$DIRECTORY
+ rsync -vrh --size-only $DIR/ $DIRECTORY/ --delete
+fi
+
+###################################
+# Sync start for kubernetes nodes #
+###################################
+
+DIRECTORY=$DIR/../sync
+if [ -d "$DIRECTORY" ]; then
+ echo "No automatic sync yet" # $DIR/../sync/sync.sh --cwl
+fi
diff --git a/kubernetes/scripts/install2.R b/cwl/scripts/install2.R
similarity index 100%
rename from kubernetes/scripts/install2.R
rename to cwl/scripts/install2.R
diff --git a/kubernetes/scripts/jobManager.sh b/cwl/scripts/jobManager.sh
similarity index 100%
rename from kubernetes/scripts/jobManager.sh
rename to cwl/scripts/jobManager.sh
diff --git a/kubernetes/scripts/jobManagerENA.sh b/cwl/scripts/jobManagerENA.sh
similarity index 100%
rename from kubernetes/scripts/jobManagerENA.sh
rename to cwl/scripts/jobManagerENA.sh
diff --git a/kubernetes/scripts/metadata.py b/cwl/scripts/metadata.py
similarity index 100%
rename from kubernetes/scripts/metadata.py
rename to cwl/scripts/metadata.py
diff --git a/kubernetes/scripts/reads.py b/cwl/scripts/reads.py
similarity index 100%
rename from kubernetes/scripts/reads.py
rename to cwl/scripts/reads.py
diff --git a/kubernetes/scripts/upload.sh b/cwl/scripts/upload.sh
similarity index 100%
rename from kubernetes/scripts/upload.sh
rename to cwl/scripts/upload.sh
diff --git a/kubernetes/scripts/upload2.sh b/cwl/scripts/upload2.sh
similarity index 100%
rename from kubernetes/scripts/upload2.sh
rename to cwl/scripts/upload2.sh