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| author | lltommy | 2020-11-11 09:56:12 +0100 |
|---|---|---|
| committer | lltommy | 2020-11-11 09:56:12 +0100 |
| commit | d6aa323b6fc7a82e45cc1df51fc72c2d547146eb (patch) | |
| tree | 6e8b77bde4dc34fab3fa8804906f3cb821f61dae /workflows/pangenome-generate/from_sparql.cwl | |
| parent | c5fe5de7e4c77bfb48b1ae2f662c2d9cc120c06e (diff) | |
| parent | c872248e43c1c66e5fed8ef341f7b4ac21d63e6f (diff) | |
| download | bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.tar.gz bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.tar.lz bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.zip | |
Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
Diffstat (limited to 'workflows/pangenome-generate/from_sparql.cwl')
| -rw-r--r-- | workflows/pangenome-generate/from_sparql.cwl | 23 |
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)] |