Merge pull request #105 from arvados/fasta-subset-from-query

Extract subset of the all-sequences fasta by running a sparql query.

Also includes some tweaks to the permalinks.

1 files changed, 23 insertions, 0 deletions

diff --git a/workflows/pangenome-generate/from_sparql.cwl b/workflows/pangenome-generate/from_sparql.cwl
new file mode 100644
index 0000000..5bc0792
--- /dev/null
+++ b/workflows/pangenome-generate/from_sparql.cwl
@@ -0,0 +1,23 @@
+cwlVersion: v1.1
+class: CommandLineTool
+requirements:
+  DockerRequirement:
+    dockerFile: |
+      FROM debian:10
+      RUN apt-get update && apt-get -yq --no-install-recommends install samtools python3-rdflib
+    dockerImageId: rdflib-and-samtools
+inputs:
+  script:
+    type: File
+    default:
+      class: File
+      location: from_sparql.py
+  metadata: File
+  fasta:
+    type: File
+    secondaryFiles: [.fai]
+  query: string
+stdout: selected.fasta
+outputs:
+  selected: stdout
+arguments: [python3, $(inputs.script), $(inputs.metadata), $(inputs.fasta), $(inputs.query)]