diff options
| -rw-r--r-- | workflows/pangenome-generate/from_sparql.cwl | 23 | ||||
| -rw-r--r-- | workflows/pangenome-generate/from_sparql.py | 8 |
2 files changed, 31 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)] diff --git a/workflows/pangenome-generate/from_sparql.py b/workflows/pangenome-generate/from_sparql.py new file mode 100644 index 0000000..4610cad --- /dev/null +++ b/workflows/pangenome-generate/from_sparql.py @@ -0,0 +1,8 @@ +from rdflib import Graph +import sys +import subprocess +g = Graph() +g.parse(sys.argv[1], format="nt") +res = g.query(sys.argv[3]) +for r in res: + subprocess.run(["samtools", "faidx", sys.argv[2], r[0]]) |