Workflow: adapter for sequence_align_and_tag

Fetched 2024-07-19 10:53:22 GMT

Some workflow engines won't stage files in our nested structure, so parse it out here

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Workflow as SVG
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Inputs

ID Type Title Doc
trimming https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/trimming_options.yml#trimming_options (Optional)
reference File

bwa-indexed reference file

unaligned https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/sequence_data.yml#sequence_data

the unaligned sequence data with readgroup information

Steps

ID Runs Label Doc
align_and_tag
../tools/sequence_align_and_tag.cwl (CommandLineTool)
align with bwa_mem and tag

Due to workflow runner limitations, use sequence_align_and_tag_adapter.cwl subworkflow to call this

Outputs

ID Type Label Doc
aligned_bam File
Permalink: https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/subworkflows/sequence_align_and_tag_adapter.cwl