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LOCALTEST.md

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Test locally

Uses the tiny test dataset in test.

Test locally, for example using miniwdl:

## End-to-end workflow (no methylation)
miniwdl run --as-me  --copy-input-files wdl/workflows/cardEndToEndVcf.wdl -i test/test.input.endtoendfastq.json

## End-to-end workflow (no methylation) cheaper by chunking reads (and preempting)
miniwdl run --as-me  --copy-input-files wdl/workflows/cardEndToEndVcf.wdl -i test/test.input.endtoendfastq.chunks.json

## End-to-end workflow (no methylation) starting with an available assembly (e.g. from shasta workflow below)
miniwdl run --as-me  --copy-input-files wdl/workflows/cardEndToEndVcf.wdl -i test/test.input.endtoendfastq.amb.json

## End-to-end workflow with uBAM input (for methylation)
miniwdl run --as-me  --copy-input-files wdl/workflows/cardEndToEndVcf.wdl -i test/test.input.endtoendfastq.ubam.json

## DV+margin workflow
miniwdl run --as-me  --copy-input-files wdl/workflows/dvMargin.wdl -i test/test.input.dvmargin.json

## shasta workflow
miniwdl run --as-me  --copy-input-files wdl/tasks/shasta.wdl -i test/test.input.shasta.json
miniwdl run --as-me  --copy-input-files wdl/tasks/shasta.wdl -i test/test.input.shasta.inmem.json

Next

  • Simulate unmapped BAMs with methylation information