knime 0.2; compatibility with cwltool and cc

Author: Christoph Jansen

.gitignore

@@ -1,2 +1,5 @@
 .idea
 outputs
+labelfree_example*
+*.log
+*.csv

README.md

@@ -2,16 +2,42 @@
 
 This is the [KNIME Labelfree Quantification](http://citar.eaas.uni-freiburg.de/citar-headless-client/?id=188b6194-ea68-4e59-88c2-61d652941e29#/container-landing-page) workflow. We have extended the original [Docker image](https://hub.docker.com/r/fbartusch/knime-labelfree-quantification/tags) to be compatible with [RED and Curious Containers](https://www.curious-containers.cc).
 
-## Run Experiment
+## Execute from Reproducible Experiment Description (RED)
 
 ```bash
 # install CC-FAICE
-pip3 install --user cc-faice==7.*
-faice --version
+pip3 install --user pipx
+pipx install cc-faice==7.*
 
-# execute RED experiment
-cd knime-labelfree-quantification-experiments
+
+# prepare
+cd knime-labelfree-quantification
+
+# execute
 faice agent red knime-labelfree-quantification.red.yml
+
+# check outputs
+ls outputs/*
+```
+
+## Alternative: Execute from Common Workflow Language (CWL)
+
+```bash
+# install CWLTool
+pip3 install --user pipx
+pipx install cwltool
+
+# prepare
+cd knime-labelfree-quantification
+curl -fOL https://s3.denbi.uni-tuebingen.de/fb-test/demo_container/cibi_user_meeting_2018/labelfree_example.tar.gz
+mkdir labelfree_example
+tar -zxvf labelfree_example.tar.gz -C labelfree_example
+
+# execute
+cwltool knime-labelfree-quantification.cwl.yml job.yml
+
+# check outputs
+ls *.csv *.log
 ```
 
 ## Resources

generate-red.py

@@ -7,6 +7,8 @@
 with open('knime-labelfree-quantification.cwl.yml') as f:
     cwl = yaml.load(f)
 
+del cwl['requirements']
+
 red = {
     'redVersion': '7',
     'cli': cwl,
@@ -69,7 +71,7 @@
         'engine': 'docker',
         'settings': {
             'image': {
-                'url': 'docker.io/deepprojects/knime-labelfree-quantification:dev'
+                'url': 'docker.io/deepprojects/knime-labelfree-quantification:0.2'
             }
         }
     }

job.yml

@@ -0,0 +1,4 @@
+input_dir:
+  class: "Directory"
+  location: "labelfree_example"
+database_name: "s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta"

knime-labelfree-quantification.cwl.yml

@@ -19,20 +19,24 @@ outputs:
   execute_log:
     type: "File"
     outputBinding:
-      glob: "/output/execute.log"
+      glob: "execute.log"
   peptide_background_quantification:
     type: "File"
     outputBinding:
-      glob: "/output/peptide_background_quantification.csv"
+      glob: "peptide_background_quantification.csv"
   protein_background_quantification:
     type: "File"
     outputBinding:
-      glob: "/output/protein_background_quantification.csv"
+      glob: "protein_background_quantification.csv"
   peptide_quantification:
     type: "File"
     outputBinding:
-      glob: "/output/peptide_quantification.csv"
+      glob: "peptide_quantification.csv"
   protein_quantification:
     type: "File"
     outputBinding:
-      glob: "/output/protein_quantification.csv"
+      glob: "protein_quantification.csv"
+
+requirements:
+  DockerRequirement:
+    dockerPull: "docker.io/deepprojects/knime-labelfree-quantification:0.2"

knime-labelfree-quantification.red.yml

@@ -14,24 +14,24 @@ cli:
       type: Directory
   outputs:
     execute_log:
-      outputBinding: {glob: /output/execute.log}
+      outputBinding: {glob: execute.log}
       type: File
     peptide_background_quantification:
-      outputBinding: {glob: /output/peptide_background_quantification.csv}
+      outputBinding: {glob: peptide_background_quantification.csv}
       type: File
     peptide_quantification:
-      outputBinding: {glob: /output/peptide_quantification.csv}
+      outputBinding: {glob: peptide_quantification.csv}
       type: File
     protein_background_quantification:
-      outputBinding: {glob: /output/protein_background_quantification.csv}
+      outputBinding: {glob: protein_background_quantification.csv}
       type: File
     protein_quantification:
-      outputBinding: {glob: /output/protein_quantification.csv}
+      outputBinding: {glob: protein_quantification.csv}
       type: File
 container:
   engine: docker
   settings:
-    image: {url: 'docker.io/deepprojects/knime-labelfree-quantification:dev'}
+    image: {url: 'docker.io/deepprojects/knime-labelfree-quantification:0.2'}
 inputs:
   database_name: s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta
   input_dir: