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Merge pull request #167 from bednarsky/166-using-sopa-as-module-in-wo…
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…rkflow-leads-to-name-error-the-name-paths-is-unknown-in-this-context

166 using sopa as module in workflow leads to name error the name paths is unknown in this context
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@quentinblampey
quentinblampey authored Jan 8, 2025
2 parents dc8978f + 2c247af commit 4972393
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Showing 2 changed files with 60 additions and 26 deletions.
83 changes: 59 additions & 24 deletions workflow/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -11,12 +11,16 @@ rule all:
paths.explorer_experiment,
paths.explorer_image,
paths.report,
params:
explorer_directory = paths.explorer_directory,
explorer_experiment = paths.explorer_experiment,
sdata_path = paths.sdata_path,
shell:
"""
echo 🎉 Successfully run sopa
echo → SpatialData output directory: {paths.sdata_path}
echo → Explorer output directory: {paths.explorer_directory}
echo → Open the result in the explorer: 'open {paths.explorer_experiment}'
echo → SpatialData output directory: {params.sdata_path}
echo → Explorer output directory: {params.explorer_directory}
echo → Open the result in the explorer: 'open {params.explorer_experiment}'
"""

rule to_spatialdata:
Expand All @@ -29,10 +33,12 @@ rule to_spatialdata:
resources:
mem_mb=128_000,
params:
args_reader = str(args['read'])
args_reader = str(args['read']),
data_path = paths.data_path,
sdata_path = paths.sdata_path,
shell:
"""
sopa read {paths.data_path} --sdata-path {paths.sdata_path} {params.args_reader}
sopa read {params.data_path} --sdata-path {params.sdata_path} {params.args_reader}
"""

checkpoint patchify_cellpose:
Expand All @@ -43,11 +49,12 @@ checkpoint patchify_cellpose:
patches = touch(paths.smk_patches),
params:
args_patchify = str(args["patchify"].where(contains="pixel")),
sdata_path = paths.sdata_path,
conda:
"sopa"
shell:
"""
sopa patchify image {paths.sdata_path} {params.args_patchify}
sopa patchify image {params.sdata_path} {params.args_patchify}
"""

checkpoint patchify_baysor:
Expand All @@ -61,11 +68,12 @@ checkpoint patchify_baysor:
args_patchify = str(args["patchify"].where(contains="micron")),
args_baysor = args.dump_baysor_patchify() if args.baysor else "",
arg_prior = "--use-prior" if args.cellpose else "",
sdata_path = paths.sdata_path,
conda:
"sopa"
shell:
"""
sopa patchify baysor {paths.sdata_path} {params.args_patchify} {params.args_baysor} {params.arg_prior}
sopa patchify baysor {params.sdata_path} {params.args_patchify} {params.args_baysor} {params.arg_prior}
"""

checkpoint patchify_comseg:
Expand All @@ -86,11 +94,12 @@ checkpoint patchify_comseg:
)),
args_comseg = args.dump_comseg_patchify() if args.comseg else "",
arg_prior = "--use-prior" if args.cellpose else "",
sdata_path = paths.sdata_path,
conda:
"sopa"
shell:
"""
sopa patchify comseg {paths.sdata_path} {params.args_patchify} {params.args_comseg} {params.arg_prior}
sopa patchify comseg {params.sdata_path} {params.args_patchify} {params.args_comseg} {params.arg_prior}
"""

rule patch_segmentation_cellpose:
Expand All @@ -103,9 +112,11 @@ rule patch_segmentation_cellpose:
"sopa"
params:
args_cellpose = str(args["segmentation"]["cellpose"]),
sdata_path = paths.sdata_path,
smk_cellpose_temp_dir = paths.smk_cellpose_temp_dir,
shell:
"""
sopa segmentation cellpose {paths.sdata_path} --patch-dir {paths.smk_cellpose_temp_dir} --patch-index {wildcards.index} {params.args_cellpose}
sopa segmentation cellpose {params.sdata_path} --patch-dir {params.smk_cellpose_temp_dir} --patch-index {wildcards.index} {params.args_cellpose}
"""

rule patch_segmentation_baysor:
Expand Down Expand Up @@ -141,13 +152,16 @@ rule patch_segmentation_comseg:
output:
paths.smk_comseg_temp_dir / "{index}" / "segmentation_polygons.json",
paths.smk_comseg_temp_dir / "{index}" / "segmentation_counts.h5ad",
params:
sdata_path = paths.sdata_path,
smk_comseg_temp_dir = paths.smk_comseg_temp_dir,
conda:
"sopa"
resources:
mem_mb=128_000,
shell:
"""
sopa segmentation comseg {paths.sdata_path} --patch-dir {paths.smk_comseg_temp_dir} --patch-index {wildcards.index}
sopa segmentation comseg {params.sdata_path} --patch-dir {params.smk_comseg_temp_dir} --patch-index {wildcards.index}
"""

def get_input_resolve(name, dirs=False):
Expand All @@ -161,11 +175,14 @@ rule resolve_cellpose:
get_input_resolve("cellpose"),
output:
touch(paths.smk_cellpose_boundaries),
params:
sdata_path = paths.sdata_path,
smk_cellpose_temp_dir = paths.smk_cellpose_temp_dir,
conda:
"sopa"
shell:
"""
sopa resolve cellpose {paths.sdata_path} --patch-dir {paths.smk_cellpose_temp_dir}
sopa resolve cellpose {params.sdata_path} --patch-dir {params.smk_cellpose_temp_dir}
"""

rule resolve_baysor:
Expand All @@ -180,11 +197,14 @@ rule resolve_baysor:
params:
args_patches_dirs = lambda _, input: " ".join(f"--patches-dirs {directory}" for directory in input.dirs),
args_min_area = args.min_area("baysor"),
sdata_path = paths.sdata_path,
smk_baysor_temp_dir = paths.smk_baysor_temp_dir,
gene_column = args.gene_column,
shell:
"""
sopa resolve baysor {paths.sdata_path} --gene-column {args.gene_column} {params.args_min_area} {params.args_patches_dirs}
sopa resolve baysor {params.sdata_path} --gene-column {params.gene_column} {params.args_min_area} {params.args_patches_dirs}
rm -r {paths.smk_baysor_temp_dir} # cleanup large baysor files
rm -r {params.smk_baysor_temp_dir} # cleanup large baysor files
"""

rule resolve_comseg:
Expand All @@ -199,11 +219,14 @@ rule resolve_comseg:
params:
args_patches_dirs=lambda _, input: " ".join(f"--patches-dirs {directory}" for directory in input.dirs),
args_min_area=args.min_area("comseg"),
sdata_path = paths.sdata_path,
smk_comseg_temp_dir = paths.smk_comseg_temp_dir,
gene_column = args.gene_column,
shell:
"""
sopa resolve comseg {paths.sdata_path} --gene-column {args.gene_column} {params.args_min_area} {params.args_patches_dirs}
sopa resolve comseg {params.sdata_path} --gene-column {params.gene_column} {params.args_min_area} {params.args_patches_dirs}
rm -r {paths.smk_comseg_temp_dir} # cleanup large comseg files
rm -r {params.smk_comseg_temp_dir} # cleanup large comseg files
"""

def get_smk_boundaries(args):
Expand All @@ -225,11 +248,12 @@ rule aggregate:
"sopa"
params:
args_aggregate = str(args["aggregate"] or ""),
sdata_path = paths.sdata_path,
resources:
mem_mb=64_000,
shell:
"""
sopa aggregate {paths.sdata_path} {params.args_aggregate}
sopa aggregate {params.sdata_path} {params.args_aggregate}
"""

rule annotate:
Expand All @@ -240,31 +264,37 @@ rule annotate:
conda:
"sopa"
resources:
partition="gpgpuq" if args['annotation']['method'] == "tangram" else "shortq",
gpu="a100:1" if args['annotation']['method'] == "tangram" else 0,
# adapted by RB, recommended by sopa author
slurm_partition = "gpu" if args['annotation']['method'] == "tangram" else "shortq",
slurm_extra = "--qos=gpu --gres=gpu:h100pcie" if args['annotation']['method'] == "tangram" else "--qos=shortq",
mem_mb = 128000,
runtime = "12h",
params:
method_name = args['annotation']['method'],
args_annotation = str(args['annotation']['args']),
sdata_path = paths.sdata_path,
shell:
"""
sopa annotate {params.method_name} {paths.sdata_path} {params.args_annotation}
sopa annotate {params.method_name} {params.sdata_path} {params.args_annotation}
"""

rule image_write:
input:
paths.sdata_zgroup,
output:
paths.explorer_image,
params:
sdata_path = paths.sdata_path,
args_explorer = str(args["explorer"].where(keys=['lazy', 'ram_threshold_gb', 'pixel_size', 'pixelsize'])),
explorer_directory = paths.explorer_directory,
conda:
"sopa"
resources:
mem_mb=64_000,
partition="longq"
params:
args_explorer = str(args["explorer"].where(keys=['lazy', 'ram_threshold_gb', 'pixel_size', 'pixelsize'])),
shell:
"""
sopa explorer write {paths.sdata_path} --output-path {paths.explorer_directory} {params.args_explorer} --mode "+i" --no-save-h5ad
sopa explorer write {params.sdata_path} --output-path {params.explorer_directory} {params.args_explorer} --mode "+i" --no-save-h5ad
"""

rule report:
Expand All @@ -274,11 +304,14 @@ rule report:
paths.annotations if args.annotate else [],
output:
paths.report,
params:
sdata_path = paths.sdata_path,
report = paths.report,
conda:
"sopa"
shell:
"""
sopa report {paths.sdata_path} {paths.report}
sopa report {params.sdata_path} {params.report}
"""

rule explorer:
Expand All @@ -294,7 +327,9 @@ rule explorer:
mem_mb=256_000,
params:
args_explorer = str(args["explorer"]),
sdata_path = paths.sdata_path,
explorer_directory = paths.explorer_directory,
shell:
"""
sopa explorer write {paths.sdata_path} --output-path {paths.explorer_directory} {params.args_explorer} --mode "-i"
sopa explorer write {params.sdata_path} --output-path {params.explorer_directory} {params.args_explorer} --mode "-i"
"""
3 changes: 1 addition & 2 deletions workflow/utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -204,8 +204,7 @@ def gene_column(self):
return self.config["segmentation"]["baysor"]["config"]["data"]["gene"]
elif "comseg" in self.config["segmentation"]:
return self.config["segmentation"]["comseg"]["config"]["gene_column"]
else:
raise ValueError("No gene column found in the config")
return "" # gene column not needed

### ComSeg related methods

Expand Down

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