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dvc.yaml
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stages:
inspect_tools:
foreach:
utilities:
name: utilities
specification: 9ec8df2a1ad7633ed0893527ca1c8c4f56426ab868a0adccea366a9fbf799898
arboreto:
name: arboreto
specification: 540b9a053e4d862bfab972735d1d62af04485c186cf5735e98748ef5b5f8b27f
NetworkInferenceJl:
name: NetworkInference.jl
specification: 3e491ce8057710cc2f0cf020b178f6315889e1b19357716b5f0da301475f9098
Rmultitool:
name: R-multitool
specification: adc703754189748fa75be2a4ec9f317f39409cfaf08eee163d7f8f59c6b511d1
do:
cmd:
- mkdir -p results/tooling
- singularity run --app manifest toolbox/bin/${item.name}.sif
>results/tooling/${item.name}.manifest
- singularity run --app specification toolbox/bin/${item.name}.sif
${item.specification}
>results/tooling/${item.name}.specification
deps:
- toolbox/bin/${item.name}.sif
outs:
- results/tooling/${item.name}.manifest
- results/tooling/${item.name}.specification
acquire_data:
cmd:
- mkdir -p results
- singularity exec toolbox/bin/utilities.sif
wget -O results/raw-inputs.zip https://ndownloader.figshare.com/files/26052149
deps:
- results/tooling/utilities.specification
- https://ndownloader.figshare.com/files/26052149
outs:
- results/raw-inputs.zip
extract_Yang_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/extract_data.sh
results/raw-inputs.zip
"noise_GRN_share/bulk_Yang/*"
results/raw/Yang
deps:
- results/raw-inputs.zip
- results/tooling/utilities.specification
outs:
- results/raw/Yang
extract_Cuomo_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/extract_data.sh
results/raw-inputs.zip
"noise_GRN_share/SC_Cuomo/*"
results/raw/Cuomo
deps:
- results/raw-inputs.zip
- results/tooling/utilities.specification
outs:
- results/raw/Cuomo
clean_Yang_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/clean_Yang.sh
results/raw/Yang
results/clean/Yang
deps:
- results/raw/Yang
- results/tooling/utilities.specification
- src/clean_Yang.sh
outs:
- results/clean/Yang
clean_Cuomo_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/clean_Cuomo.sh
results/raw/Cuomo
results/clean/Cuomo
deps:
- results/raw/Cuomo
- results/tooling/utilities.specification
- src/clean_Cuomo.sh
outs:
- results/clean/Cuomo
denoise_Yang_data:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/denoise.sh
results/clean/Yang
counts_raw.csv
results/denoised/Yang
logs/denoised/Yang
deps:
- results/clean/Yang
- results/tooling/R-multitool.specification
- src/denoise.sh
- src/denoise.R
outs:
- results/denoised/Yang
denoise_Cuomo_data:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/denoise.sh
results/clean/Cuomo
counts_raw_day2.csv
results/denoised/Cuomo
logs/denoised/Cuomo
deps:
- results/clean/Cuomo
- results/tooling/R-multitool.specification
- src/denoise.sh
- src/denoise.R
outs:
- results/denoised/Cuomo
slice_Yang_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/slice.sh
results/denoised/Yang
results/sliced/Yang
deps:
- results/denoised/Yang
- results/tooling/utilities.specification
- src/slice.sh
outs:
- results/sliced/Yang
fuse_Yang_data:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/fuse_samples_foreach.sh
results/denoised/Yang
results/clean/Yang/samples.csv
results/fused/Yang
deps:
- results/clean/Yang
- results/denoised/Yang
- results/tooling/R-multitool.specification
- src/fuse_samples_foreach.sh
- src/fuse_samples.R
outs:
- results/fused/Yang
slice_Yang_fused_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/slice.sh
results/fused/Yang
results/sliced_fused/Yang
deps:
- results/fused/Yang
- results/tooling/utilities.specification
- src/slice.sh
outs:
- results/sliced_fused/Yang
slice_Cuomo_data:
cmd: singularity exec toolbox/bin/utilities.sif sh src/slice.sh
results/denoised/Cuomo
results/sliced/Cuomo
deps:
- results/denoised/Cuomo
- results/tooling/utilities.specification
- src/slice.sh
outs:
- results/sliced/Cuomo
infer:
foreach:
Yang/NetworkInference.jl/CLR: { data: Yang, tool: NetworkInference.jl, src: NetworkInference.jl, cmd: "julia src/inference/NetworkInference.jl/infer_network.jl CLR" }
Yang/NetworkInference.jl/MI: { data: Yang, tool: NetworkInference.jl, src: NetworkInference.jl, cmd: "julia src/inference/NetworkInference.jl/infer_network.jl MI" }
Yang/NetworkInference.jl/PIDC: { data: Yang, tool: NetworkInference.jl, src: NetworkInference.jl, cmd: "julia src/inference/NetworkInference.jl/infer_network.jl PIDC" }
Yang/NetworkInference.jl/PUC: { data: Yang, tool: NetworkInference.jl, src: NetworkInference.jl, cmd: "julia src/inference/NetworkInference.jl/infer_network.jl PUC" }
Yang/GENIE3-R: { data: Yang, tool: R-multitool, src: GENIE3-R, cmd: "Rscript src/inference/GENIE3-R/infer_network.R" }
Yang/LEAP: { data: Yang, tool: R-multitool, src: LEAP, cmd: "Rscript src/inference/LEAP/infer_network.R" }
Yang/GRNBoost2: { data: Yang, tool: arboreto, src: GRNBoost2, cmd: "python src/inference/GRNBoost2/infer_network.py" }
Cuomo/NetworkInference.jl/CLR: { data: Cuomo, tool: NetworkInference.jl, src: NetworkInference.jl, cmd: "julia src/inference/NetworkInference.jl/infer_network.jl CLR" }
Cuomo/NetworkInference.jl/MI: { data: Cuomo, tool: NetworkInference.jl, src: NetworkInference.jl, cmd: "julia src/inference/NetworkInference.jl/infer_network.jl MI" }
Cuomo/NetworkInference.jl/PIDC: { data: Cuomo, tool: NetworkInference.jl, src: NetworkInference.jl, cmd: "julia src/inference/NetworkInference.jl/infer_network.jl PIDC" }
Cuomo/NetworkInference.jl/PUC: { data: Cuomo, tool: NetworkInference.jl, src: NetworkInference.jl, cmd: "julia src/inference/NetworkInference.jl/infer_network.jl PUC" }
Cuomo/GENIE3-R: { data: Cuomo, tool: R-multitool, src: GENIE3-R, cmd: "Rscript src/inference/GENIE3-R/infer_network.R" }
Cuomo/GRNBoost2: { data: Cuomo, tool: arboreto, src: GRNBoost2, cmd: "python src/inference/GRNBoost2/infer_network.py" }
do:
cmd: singularity exec toolbox/bin/${item.tool}.sif sh src/inference/infer_foreach_slice.sh
results/sliced/${item.data}
results/networks/${key}
logs/networks/${key}
${item.cmd}
deps:
- results/sliced/${item.data}
- results/tooling/${item.tool}.specification
- src/inference/infer_foreach_slice.sh
- src/inference/${item.src}
outs:
- results/networks/${key}
analyze:
foreach:
Yang/NetworkInference.jl/CLR: { loader: load_network_inference_jl_network.function.R }
Yang/NetworkInference.jl/MI: { loader: load_network_inference_jl_network.function.R }
Yang/NetworkInference.jl/PIDC: { loader: load_network_inference_jl_network.function.R }
Yang/NetworkInference.jl/PUC: { loader: load_network_inference_jl_network.function.R }
Yang/GENIE3-R: { loader: load_genie3r_network.function.R }
Yang/LEAP: { loader: load_leap_network.function.R }
Yang/GRNBoost2: { loader: load_grnboost2_network.function.R }
Cuomo/NetworkInference.jl/CLR: { loader: load_network_inference_jl_network.function.R }
Cuomo/NetworkInference.jl/MI: { loader: load_network_inference_jl_network.function.R }
Cuomo/NetworkInference.jl/PIDC: { loader: load_network_inference_jl_network.function.R }
Cuomo/NetworkInference.jl/PUC: { loader: load_network_inference_jl_network.function.R }
Cuomo/GENIE3-R: { loader: load_genie3r_network.function.R }
Cuomo/GRNBoost2: { loader: load_grnboost2_network.function.R }
do:
cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
results/networks/${key}
results/analysis/${key}
logs/analysis/${key}
Rscript src/analysis/analyze_for_network_variants.R src/analysis/data_variants.csv src/analysis/${item.loader} png
deps:
- results/networks/${key}
- results/tooling/R-multitool.specification
- src/analysis/analyze_foreach_slice.sh
- src/analysis/analyze_for_network_variants.R
- src/analysis/data_variants.csv
- src/analysis/${item.loader}
outs:
- results/analysis/${key}