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Remove/update references to MELT #857

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71f9e39
remove/update references to melt
epiercehoffman Aug 19, 2025
456f250
remove docker scripts readme in favor of website
epiercehoffman Aug 19, 2025
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2 changes: 0 additions & 2 deletions inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl
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Expand Up @@ -6,8 +6,6 @@
"GATKSVPipelineBatch.gcnv_model_tars" : {{ test_batch.gcnv_model_tars | tojson }},
"GATKSVPipelineBatch.qc_definitions" : {{ test_batch.qc_definitions | tojson }},

"GATKSVPipelineBatch.melt_docker" : {{ dockers.melt_docker | tojson }},

"GATKSVPipelineBatch.manta_docker": {{ dockers.manta_docker | tojson }},
"GATKSVPipelineBatch.wham_docker": {{ dockers.wham_docker | tojson }},
"GATKSVPipelineBatch.cnmops_docker": {{ dockers.cnmops_docker | tojson }},
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1 change: 0 additions & 1 deletion inputs/templates/test/GatherSampleEvidence/GatherSampleEvidence.json.tmpl
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Expand Up @@ -30,7 +30,6 @@
"GatherSampleEvidence.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }},
"GatherSampleEvidence.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
"GatherSampleEvidence.manta_docker": {{ dockers.manta_docker | tojson }},
"GatherSampleEvidence.melt_docker" : {{ dockers.melt_docker | tojson }},
"GatherSampleEvidence.scramble_docker" : {{ dockers.scramble_docker | tojson }},
"GatherSampleEvidence.wham_docker": {{ dockers.wham_docker | tojson }},
"GatherSampleEvidence.genomes_in_the_cloud_docker" : {{ dockers.genomes_in_the_cloud_docker | tojson }},
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47 changes: 0 additions & 47 deletions scripts/docker/README.md
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This file was deleted.

11 changes: 0 additions & 11 deletions website/docs/advanced/cromwell/quick_start.md
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Expand Up @@ -23,17 +23,6 @@ We provide options for building example inputs that you may use as a reference
to configure a Terra workspace or Cromwell submissions (advanced) with your own data.
Please refer to [this page](/docs/advanced/build_inputs) for instructions on how to build these inputs.

### MELT
Important: The example input files contain MELT inputs that are NOT public
(see [Requirements](https://github.com/broadinstitute/gatk-sv#requirements)). These include:

- `GATKSVPipelineSingleSample.melt_docker` and `GATKSVPipelineBatch.melt_docker` - MELT docker URI
(see [Docker readme](https://github.com/talkowski-lab/gatk-sv-v1/blob/master/dockerfiles/README.md))
- `GATKSVPipelineSingleSample.ref_std_melt_vcfs` - Standardized MELT VCFs ([GatherBatchEvidence](/docs/modules/gbe))
The input values are provided only as an example and are not publicly accessible.
- In order to include MELT, these values must be provided by the user. MELT can be
disabled by deleting these inputs and setting `GATKSVPipelineBatch.use_melt` to false.

### Execution

```shell
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2 changes: 1 addition & 1 deletion website/docs/execution/joint.md
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Expand Up @@ -58,7 +58,7 @@ The following are the main pipeline outputs. For more information on the outputs
The following workflows and Jupyter notebooks are included in this workspace, to be executed in this order:

1. `01-GatherSampleEvidence`: Per-sample SV evidence collection, including calls from a configurable set of
algorithms (Manta, MELT, and Wham), read depth (RD), split read positions (SR), and discordant pair positions (PE).
algorithms (Manta, Scramble, and Wham), read depth (RD), split read positions (SR), and discordant pair positions (PE).
2. `02-EvidenceQC`: Dosage bias scoring and ploidy estimation, run on preliminary batches
3. [Notebook] `SampleQC.ipynb`: Interactively perform sample QC and filtering using outputs from `02-EvidenceQC`
4. [Notebook] `Batching.ipynb`: Create batches for subsequent steps. For cohorts >500 samples or smaller heterogeneous cohorts
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