updated experiment for RED 8

Author: Christoph Jansen

README.md

@@ -7,14 +7,14 @@ This is the [KNIME Labelfree Quantification](http://citar.eaas.uni-freiburg.de/c
 ```bash
 # install CC-FAICE
 pip3 install --user pipx
-pipx install cc-faice==7.*
+pipx install cc-faice==8.*
 
 
 # prepare
 cd knime-labelfree-quantification
 
 # execute
-faice agent red knime-labelfree-quantification.red.yml
+faice exec knime-labelfree-quantification.red.yml
 
 # check outputs
 ls outputs/*

generate-red-and-job.py

@@ -60,7 +60,7 @@
 
 
 red = {
-    'redVersion': '7',
+    'redVersion': '8',
     'cli': cwl,
     'inputs': {
         'input_dir': {
@@ -83,6 +83,10 @@
                 'url': docker_image_url
             }
         }
+    },
+    'execution': {
+        'engine': 'ccfaice',
+        'settings': {}
     }
 }
 

knime-labelfree-quantification.cwl.yml

@@ -39,4 +39,4 @@ outputs:
 
 requirements:
   DockerRequirement:
-    dockerPull: "docker.io/deepprojects/knime-labelfree-quantification:0.2"
+    dockerPull: "docker.io/deepprojects/knime-labelfree-quantification:0.3"

knime-labelfree-quantification.red.yml

@@ -31,7 +31,10 @@ cli:
 container:
   engine: docker
   settings:
-    image: {url: 'docker.io/deepprojects/knime-labelfree-quantification:0.2'}
+    image: {url: 'docker.io/deepprojects/knime-labelfree-quantification:0.3'}
+execution:
+  engine: ccfaice
+  settings: {}
 inputs:
   database_name: s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta
   input_dir:
@@ -65,4 +68,4 @@ inputs:
         class: File}
       - {basename: uniprot-s-pyogenes-sf370-plus-potato-and-human-spike-ins.fasta.psq,
         class: File}
-redVersion: '7'
+redVersion: '8'