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Add support for other conda env #262

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19 changes: 10 additions & 9 deletions workflow/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ from src import WorkflowPaths, Args, validate_config
config = validate_config(config) # validate the Snakemake config
paths = WorkflowPaths(config) # object handling the paths to the files that will be created
args = Args(paths, config) # object handling the arguments passed to the workflow
conda_env = "YOUR_ENVIRONMENT_NAME" # conda environment to use for the rules

### Segmentation rules
include: "rules/utils.smk"
Expand Down Expand Up @@ -38,7 +39,7 @@ rule to_spatialdata:
output:
paths.sdata_zgroup if paths.data_path else [],
conda:
"sopa"
conda_env
params:
reader = args['read'].as_cli(),
data_path = paths.data_path,
Expand All @@ -54,7 +55,7 @@ rule tissue_segmentation:
output:
touch(paths.segmentation_done("tissue")),
conda:
"sopa"
conda_env
params:
tissue_segmentation = args["segmentation"]["tissue"].as_cli(),
sdata_path = paths.sdata_path,
Expand All @@ -74,7 +75,7 @@ checkpoint patchify_image:
patchify_image = args["patchify"].as_cli(contains="pixel"),
sdata_path = paths.sdata_path,
conda:
"sopa"
conda_env
shell:
"""
sopa patchify image {params.sdata_path} {params.patchify_image}
Expand All @@ -92,7 +93,7 @@ checkpoint patchify_transcripts:
patchify_transcripts = args.patchify_transcripts(),
sdata_path = paths.sdata_path,
conda:
"sopa"
conda_env
shell:
"""
sopa patchify transcripts {params.sdata_path} {params.patchify_transcripts}
Expand All @@ -104,7 +105,7 @@ rule aggregate:
output:
touch(paths.smk_aggregation),
conda:
"sopa"
conda_env
params:
aggregate = args["aggregate"].as_cli(),
sdata_path = paths.sdata_path,
Expand All @@ -119,7 +120,7 @@ rule annotate:
output:
directory(paths.annotations),
conda:
"sopa"
conda_env
resources:
partition="gpgpuq" if args['annotation']['method'] == "tangram" else "shortq",
gpu="a100:1" if args['annotation']['method'] == "tangram" else 0,
Expand All @@ -138,7 +139,7 @@ rule explorer_raw:
output:
touch(paths.smk_explorer_raw),
conda:
"sopa"
conda_env
params:
explorer = args["explorer"].as_cli(keys=['lazy', 'ram_threshold_gb', 'pixel_size', 'pixelsize']),
sdata_path = paths.sdata_path,
Expand All @@ -156,7 +157,7 @@ rule explorer:
output:
paths.explorer_experiment,
conda:
"sopa"
conda_env
params:
explorer = args["explorer"].as_cli(),
sdata_path = paths.sdata_path,
Expand All @@ -177,7 +178,7 @@ rule report:
sdata_path = paths.sdata_path,
report = paths.report,
conda:
"sopa"
conda_env
shell:
"""
sopa report {params.sdata_path} {params.report}
Expand Down
4 changes: 2 additions & 2 deletions workflow/rules/cellpose.smk
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Expand Up @@ -5,7 +5,7 @@ rule patch_segmentation_cellpose:
output:
paths.temp_dir("cellpose") / "{index}.parquet",
conda:
"sopa"
conda_env
params:
cellpose = args["segmentation"]["cellpose"].as_cli(),
sdata_path = paths.sdata_path,
Expand All @@ -21,7 +21,7 @@ rule resolve_cellpose:
output:
touch(paths.segmentation_done("cellpose")),
conda:
"sopa"
conda_env
params:
sdata_path = paths.sdata_path,
shell:
Expand Down
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