Merge branch 'master' into patch-3

1 files changed, 50 insertions, 0 deletions

diff --git a/workflows/pangenome-generate/relabel-seqs.cwl b/workflows/pangenome-generate/relabel-seqs.cwl
new file mode 100644
index 0000000..c1f17a4
--- /dev/null
+++ b/workflows/pangenome-generate/relabel-seqs.cwl
@@ -0,0 +1,50 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+  readsFA: File[]
+  subjects: string[]
+  script:
+    type: File
+    default: {class: File, location: relabel-seqs.py}
+    inputBinding: {}
+outputs:
+  relabeledSeqs:
+    type: File
+    outputBinding:
+      glob: relabeledSeqs.fasta
+  originalLabels:
+    type: File
+    outputBinding:
+      glob: originalLabels.ttl
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing: |
+          ${
+          var i = 0;
+          var b = 1;
+          var out = [];
+          for (; i < inputs.readsFA.length; i++) {
+            var block = [];
+            var sub = [];
+            for (; i < (b*150) && i < inputs.readsFA.length; i++) {
+              block.push(inputs.readsFA[i]);
+              sub.push(inputs.subjects[i]);
+            }
+            out.push({
+              entryname: "block"+b,
+              entry: JSON.stringify(block)
+            });
+            out.push({
+              entryname: "subs"+b,
+              entry: JSON.stringify(sub)
+            });
+            b++;
+          }
+          return out;
+          }
+hints:
+  DockerRequirement:
+    dockerPull: commonworkflowlanguage/cwltool_module
+stdout:
+baseCommand: [python]