Add query-to-gfa workflow

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

1 files changed, 32 insertions, 0 deletions

diff --git a/workflows/pangenome-generate/query-to-gfa.cwl b/workflows/pangenome-generate/query-to-gfa.cwl
new file mode 100644
index 0000000..2f3a20a
--- /dev/null
+++ b/workflows/pangenome-generate/query-to-gfa.cwl
@@ -0,0 +1,32 @@
+cwlVersion: v1.1
+class: Workflow
+requirements:
+  SubworkflowFeatureRequirement: {}
+inputs:
+  metadata: File
+  fasta:
+    type: File
+    secondaryFiles: [.fai]
+  query: string
+outputs:
+  odgiGraph:
+    type: File
+    outputSource: make-gfa/odgiGraph
+  spoaGFA:
+    type: File
+    outputSource: make-gfa/spoaGFA
+  readsMergeDedupSortedByQualAndLen:
+    type: File
+    outputSource: make-gfa/readsMergeDedupSortedByQualAndLen
+  mergedMetadata:
+    type: File
+    outputSource: make-gfa/mergedMetadata
+steps:
+  get-subset:
+    run: from_sparql.cwl
+    in: {metadata: metadata, query: query, fasta: fasta}
+    out: [selected]
+  make-gfa:
+    run: pangenome-generate_spoa.cwl
+    in: {metadata: metadata, seqs: get-subset/selected}
+    out: [odgiGraph, spoaGFA, readsMergeDedupSortedByQualAndLen, mergedMetadata]