linux-sort/bedtools/STAR fixes

Author: portah

tools/STAR.cwl

@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
-# "@base": "https://w3id.org/cwl/cwl#"
 
 "@context":
+  "cwl": "https://w3id.org/cwl/cwl#"
   "foaf": "http://xmlns.com/foaf/0.1/"
   "doap": "http://usefulinc.com/ns/doap"
   "adms": "http://purl.org/adms/"
@@ -23,18 +23,17 @@ adms:Asset:
     doap:license: "GPL"
     doap:category: "commandline tool"
     doap:programming-language: "C++"
-    - foaf:Organization:
-      foaf:name: "Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"
-    - foaf:Organization:
-      foaf:name: "2Pacific Biosciences, Menlo Park, CA, USA"
+    foaf:Organization:
+      - foaf:name: "Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"
+      - foaf:name: "2Pacific Biosciences, Menlo Park, CA, USA"
     foaf:publications:
       - foaf:title: "(Dobin et al., 2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics."
         foaf:homepage: "http://www.ncbi.nlm.nih.gov/pubmed/23104886"
     doap:developer:
       foaf:Person:
-      foaf:name: "Alexander Dobin"
-      foaf:mbox: "mailto:dobin at cshl.edu"
-      foaf:fundedBy: "This work was funded by NHGRI (NIH) grant U54HG004557"
+        foaf:name: "Alexander Dobin"
+        foaf:mbox: "mailto:dobin at cshl.edu"
+        foaf:fundedBy: "This work was funded by NHGRI (NIH) grant U54HG004557"
   adms:AssetDistribution:
     doap:name: "STAR.cwl"
     doap:description: "Developed for CWL consortium http://commonwl.org/"

tools/bedtools-genomecov.cwl

@@ -1,6 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 "@context":
+  "cwl": "https://w3id.org/cwl/cwl#"
   "foaf": "http://xmlns.com/foaf/0.1/"
   "doap": "http://usefulinc.com/ns/doap"
   "adms": "http://purl.org/adms/"
@@ -30,7 +31,7 @@ adms:Asset:
       - foaf:title: "(Quinlan and Hall, 2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics."
         foaf:homepage: "http://www.ncbi.nlm.nih.gov/pubmed/20110278"
     doap:maintainer:
-      - foaf:Person:
+      foaf:Person:
         foaf:name: "Aaron R. Quinlan"
         foaf:mbox: "aaronquinlan at gmail.com"
   adms:AssetDistribution:

tools/jobs/linux-sort-job.json

@@ -1,8 +1,9 @@
 {
-    "input": {
-        "class": "File",
-        "path": "../test-files/SRR1031972.bedGraph"
-    },
+    "input": [{
+        "path": "../test-files/SRR1031972.bedGraph",
+        "class": "File"
+    }],
+    "output": "./test-files/SRR1031972.bedGraph.sorted",
     "key": [
         "1,1",
         "2,2n"

tools/linux-sort.cwl

@@ -1,5 +1,12 @@
 #!/usr/bin/env cwl-runner
 
+"@context":
+  "cwl": "https://w3id.org/cwl/cwl#"
+  "foaf": "http://xmlns.com/foaf/0.1/"
+  "doap": "http://usefulinc.com/ns/doap"
+  "adms": "http://purl.org/adms/"
+  "admssw": "http://purl.org/adms/sw/"
+
 adms:Asset:
   admssw:SoftwareProject:
     doap:name: "sort"
@@ -9,15 +16,13 @@ adms:Asset:
       - doap:revision: "5.93"
     doap:license: "GPL"
     doap:category: "commandline tool"
-    - doap:developer:
-      foaf:Person:
-      foaf:name: "Mike Haertel"
-    - doap:developer:
-      foaf:Person:
-      foaf:name: "Paul Eggert"
-    - doap:developer:
-      foaf:Person:
-      foaf:mbox: "bug-coreutils@gnu.org"
+    doap:developer:
+      - foaf:Person:
+        foaf:name: "Mike Haertel"
+      - foaf:Person:
+        foaf:name: "Paul Eggert"
+      - foaf:Person:
+        foaf:mbox: "bug-coreutils@gnu.org"
   adms:AssetDistribution:
     doap:name: "linux-sort.cwl"
     doap:description: "Developed for CWL consortium http://commonwl.org/"
@@ -79,7 +84,7 @@ outputs:
     outputBinding:
       glob: $(inputs.output)
 
-stdout:
+stdout: $(inputs.output)
 baseCommand: ["sort"]
 #$(inputs.input.path.split('/').slice(-1)[0] + '.sorted')