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| author | Peter Amstutz | 2020-07-03 20:45:17 +0000 |
|---|---|---|
| committer | Peter Amstutz | 2020-07-03 20:47:14 +0000 |
| commit | 535b8017ddd27a9db683f6d29368258b5c48cf5a (patch) | |
| tree | 521a3e446f0eb9cbdc6e8736a13706c8141f8351 /scripts/import_from_genbank.cwl | |
| parent | 841af02eaa45c1b7395d5f4e4711de3c3661c146 (diff) | |
| download | bh20-seq-resource-535b8017ddd27a9db683f6d29368258b5c48cf5a.tar.gz bh20-seq-resource-535b8017ddd27a9db683f6d29368258b5c48cf5a.tar.lz bh20-seq-resource-535b8017ddd27a9db683f6d29368258b5c48cf5a.zip | |
Improving genbank import workflow
Diffstat (limited to 'scripts/import_from_genbank.cwl')
| -rw-r--r-- | scripts/import_from_genbank.cwl | 27 |
1 files changed, 27 insertions, 0 deletions
diff --git a/scripts/import_from_genbank.cwl b/scripts/import_from_genbank.cwl new file mode 100644 index 0000000..dcf9acb --- /dev/null +++ b/scripts/import_from_genbank.cwl @@ -0,0 +1,27 @@ +cwlVersion: v1.1 +class: Workflow +inputs: + existing_metadata_from_nuccore: + type: Directory? +outputs: [] +requirements: + ScatterFeatureRequirement: {} +steps: + fetch_from_genbank: + in: + existing_metadata_from_nuccore: existing_metadata_from_nuccore + out: [fasta_and_yaml, metadata_from_nuccore, accessions] + run: fetch_from_genbank.cwl + split_into_arrays: + in: + dir: fetch_from_genbank/fasta_and_yaml + out: [fasta, metadata] + run: split_into_arrays.cwl + upload: + in: + fasta: split_into_arrays/fasta + metadata: split_into_arrays/metadata + out: [] + scatter: [fasta, metadata] + scatterMethod: dotproduct + run: upload.cwl |