Move workflows into main repo

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

1 files changed, 57 insertions, 0 deletions

diff --git a/workflows/pangenome-generate/pangenome-generate.cwl b/workflows/pangenome-generate/pangenome-generate.cwl
new file mode 100644
index 0000000..2710743
--- /dev/null
+++ b/workflows/pangenome-generate/pangenome-generate.cwl
@@ -0,0 +1,57 @@
+cwlVersion: v1.1
+class: Workflow
+inputs:
+  inputReads: File[]
+  metadata: File[]
+  metadataSchema: File
+  subjects: string[]
+outputs:
+  odgiGraph:
+    type: File
+    outputSource: buildGraph/odgiGraph
+  odgiPNG:
+    type: File
+    outputSource: vizGraph/odgiPNG
+  seqwishGFA:
+    type: File
+    outputSource: induceGraph/seqwishGFA
+  odgiRDF:
+    type: File
+    outputSource: odgi2rdf/rdf
+  mergedMetadata:
+    type: File
+    outputSource: mergeMetadata/merged
+steps:
+  dedup:
+    in: {readsFA: inputReads}
+    out: [readsMergeDedup]
+    run: seqkit-rmdup.cwl
+  overlapReads:
+    in: {readsFA: dedup/readsMergeDedup}
+    out: [readsPAF]
+    run: minimap2.cwl
+  induceGraph:
+    in:
+      readsFA: dedup/readsMergeDedup
+      readsPAF: overlapReads/readsPAF
+    out: [seqwishGFA]
+    run: seqwish.cwl
+  buildGraph:
+    in: {inputGFA: induceGraph/seqwishGFA}
+    out: [odgiGraph]
+    run: odgi-build.cwl
+  vizGraph:
+    in: {inputODGI: buildGraph/odgiGraph}
+    out: [odgiPNG]
+    run: odgi-viz.cwl
+  odgi2rdf:
+    in: {odgi: buildGraph/odgiGraph}
+    out: [rdf]
+    run: odgi_to_rdf.cwl
+  mergeMetadata:
+    in:
+      metadata: metadata
+      metadataSchema: metadataSchema
+      subjects: subjects
+    out: [merged]
+    run: merge-metadata.cwl