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| author | Peter Amstutz | 2020-11-09 17:32:05 -0500 |
|---|---|---|
| committer | GitHub | 2020-11-09 17:32:05 -0500 |
| commit | 74d46196ae69c0c557f64593910ada48d84b3654 (patch) | |
| tree | 57c7df946e1aa1f2054eb49379439ebee4d4c0e6 /workflows/pangenome-generate/from_sparql.cwl | |
| parent | b311e2ec0f1d02cf16152855dd8bdd760ed4578b (diff) | |
| parent | 98a80bd64d8a495b8fddffdef6e07e5a3fbea1e3 (diff) | |
| download | bh20-seq-resource-74d46196ae69c0c557f64593910ada48d84b3654.tar.gz bh20-seq-resource-74d46196ae69c0c557f64593910ada48d84b3654.tar.lz bh20-seq-resource-74d46196ae69c0c557f64593910ada48d84b3654.zip | |
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.
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)] |