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use store_true for --use_preset #79

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merged 1 commit into from
Jul 16, 2024
Merged

use store_true for --use_preset #79

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11 changes: 6 additions & 5 deletions workflow/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,8 @@
## Dependencies

All dependent software is included in our Docker/Singularity container.
Users of other installation approaches may install the dependencies using conda, pre-built binary, or building from source.
Users of other installation approaches may install the dependencies using
conda, pre-built binary, or building from source.

- Aligner: [minimap2](https://github.com/lh3/minimap2)/[winnowmap2](https://github.com/marbl/Winnowmap)/[bwa mem](https://github.com/lh3/bwa)/[Bowtie 2](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml)
- samtools, bgzip
Expand All @@ -24,7 +25,7 @@ python leviosam2.py \
-fi bt2/grch38.fna \
--sequence_type ilmn_pe \
-a bowtie2 \
--use_preset True \
--use_preset \
--lift_bed_commit_source suppress_annotations.bed \ # optional
--lift_bed_defer_target defer_annotations.bed # optional
```
Expand Down Expand Up @@ -56,7 +57,7 @@ python leviosam2.py \
-fi bwa/grch38.fna \
--sequence_type ilmn_pe \
-a bwamem \
--use_preset True \
--use_preset \
--lift_bed_commit_source suppress_annotations.bed \ # optional
--lift_bed_defer_target defer_annotations.bed # optional
```
Expand Down Expand Up @@ -96,7 +97,7 @@ python leviosam2.py \
-f grch38.fna \
--sequence_type pb_hifi \
-a minimap2 \
--use_preset True \
--use_preset \
--lift_realign_config ../configs/pacbio_all.yaml \
--lift_bed_commit_source suppress_annotations.bed # optional
```
Expand Down Expand Up @@ -126,7 +127,7 @@ python leviosam2.py \
-f grch38.fna \
--sequence_type ont \
-a minimap2 \
--use_preset True \
--use_preset \
--lift_realign_config ../configs/ont_all.yaml \
--lift_bed_commit_source suppress_annotations.bed # optional
```
Expand Down
3 changes: 1 addition & 2 deletions workflow/leviosam2.py
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Expand Up @@ -231,8 +231,7 @@ def parse_args() -> argparse.Namespace:
# )
parser.add_argument(
"--use_preset",
type=bool,
default=True,
action="store_true",
help="Use default workflow parameters",
)
parser.add_argument(
Expand Down
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