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Merged
DonFreed merged 3 commits into from
Apr 4, 2026
Merged

Merge dev changes #23

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b958e72
Remove the earlier `pangenome` pipeline
DonFreed Apr 4, 2026
3a0d868
Rename `sentieon-pangenome` to `dnascope-pangenome`.
DonFreed Apr 4, 2026
eff34db
Documentation updates
DonFreed Apr 4, 2026
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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ The `sentieon-cli` supports the following global arguments:
- [**DNAscope**](https://support.sentieon.com/docs/sentieon_cli/#dnascope) - DNAscope pipeline implementation for germline SNV and indel calling from short read data.
- [**DNAscope LongRead**](https://support.sentieon.com/docs/sentieon_cli/#dnascope-longread) - DNAscope LongRead pipeline implementations for germline SNV and indel calling from long read data.
- [**DNAscope Hybrid**](https://support.sentieon.com/docs/sentieon_cli/#dnascope-hybrid) - DNAscope short-long-hybrid pipeline.
- [**Sentieon Pangenome**](https://support.sentieon.com/docs/sentieon_cli/#sentieon-pangenome) - Sentieon pangenome alignment and variant calling. Our recommended pipeline for short-read small variant calling.
- [**DNAscope Pangenome**](https://support.sentieon.com/docs/sentieon_cli/#sentieon-pangenome) - DNAscope pangenome alignment and variant calling. Our recommended pipeline for short-read small variant calling.

## License
Unless otherwise indicated, files in this repository are licensed under a BSD 2-Clause License.
244 changes: 0 additions & 244 deletions docs/pangenome.md
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17 changes: 6 additions & 11 deletions sentieon_cli/__init__.py
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Expand Up @@ -2,7 +2,6 @@
from .dnascope import DNAscopePipeline
from .dnascope_hybrid import DNAscopeHybridPipeline
from .dnascope_longread import DNAscopeLRPipeline
from .pangenome import PangenomePipeline
from .sentieon_pangenome import SentieonPangenome
from .util import __version__

Expand Down Expand Up @@ -51,17 +50,13 @@ def main():
pipeline.add_arguments(dnascope_hybrid_subparser)
dnascope_hybrid_subparser.set_defaults(pipeline=pipeline.main)

# Pangenome parser
pipeline = PangenomePipeline()
pangenome_subparser = subparsers.add_parser("pangenome")
pipeline.add_arguments(pangenome_subparser)
pangenome_subparser.set_defaults(pipeline=pipeline.main)

# Sentieon pangenome
# DNAscope pangenome
pipeline = SentieonPangenome()
sentieon_pangenome_subparser = subparsers.add_parser("sentieon-pangenome")
pipeline.add_arguments(sentieon_pangenome_subparser)
sentieon_pangenome_subparser.set_defaults(pipeline=pipeline.main)
dnascope_pangenome_subparser = subparsers.add_parser(
"dnascope-pangenome", aliases=["sentieon-pangenome"]
)
pipeline.add_arguments(dnascope_pangenome_subparser)
dnascope_pangenome_subparser.set_defaults(pipeline=pipeline.main)

args = parser.parse_args()
args.pipeline(args)
Expand Down
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