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Snakefile
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rule all:
input:
"confusion/ukdf.csv",
"confusion/SVC/Lake_SVC_confusion.csv",
"confusion/SVC/Liao_SVC_confusion.csv",
"confusion/SVC/Menon_SVC_confusion.csv",
"confusion/SVC/Young_SVC_confusion.csv",
"confusion/SVC/Wu_SVC_confusion.csv",
"confusion/RandomForest/Lake_RandomForest_confusion.csv",
"confusion/RandomForest/Liao_RandomForest_confusion.csv",
"confusion/RandomForest/Menon_RandomForest_confusion.csv",
"confusion/RandomForest/Young_RandomForest_confusion.csv",
"confusion/RandomForest/Wu_RandomForest_confusion.csv",
"confusion/MLP/Lake_MLP_confusion.csv",
"confusion/MLP/Liao_MLP_confusion.csv",
"confusion/MLP/Menon_MLP_confusion.csv",
"confusion/MLP/Young_MLP_confusion.csv",
"confusion/MLP/Wu_MLP_confusion.csv",
"confusion/KNeighbor/Lake_KNeighbor_confusion.csv",
"confusion/KNeighbor/Liao_KNeighbor_confusion.csv",
"confusion/KNeighbor/Menon_KNeighbor_confusion.csv",
"confusion/KNeighbor/Young_KNeighbor_confusion.csv",
"confusion/KNeighbor/Wu_KNeighbor_confusion.csv",
"confusion/XGB/Lake_XGB_confusion.csv",
"confusion/XGB/Liao_XGB_confusion.csv",
"confusion/XGB/Menon_XGB_confusion.csv",
"confusion/XGB/Young_XGB_confusion.csv",
"confusion/XGB/Wu_XGB_confusion.csv",
"scores/Median_F1_heatmap.pdf",
"confusion/Percent_Unknown_heatmap.pdf",
"scores/F1_scores.csv"
rule IntegrateAll:
input:
data = "data/MergedObject.RDS"
output:
int = "data/integratedobject.h5ad"
log: "data/IntegrateAll.log"
singularity: "docker://sblough18/seurat-integrate:latest"
shell:
"Rscript Scripts/IntegrateAll.R "
"{input.data} "
"&> {log} "
rule QualityControl:
input:
data = "data/integratedobject.h5ad"
output:
tfval = "data/cellstouse.csv",
unkn = "confusion/UnknownpercentsvmQCconfusion.csv"
log: "data/QC.log"
singularity: "docker://sblough18/svm:latest"
shell:
"python3 Scripts/QualityControl.py "
"{input.data} "
"&> {log} "
rule IntegrateSome:
input:
data = "data/MergedObject.RDS",
tfval = "data/cellstouse.csv"
output:
int1 = "data/svmtest1.h5ad",
int2 = "data/svmtest2.h5ad",
int3 = "data/svmtest3.h5ad",
int4 = "data/svmtest4.h5ad",
int5 = "data/svmtest5.h5ad"
log: "data/IntegrateSome.log"
singularity: "docker://sblough18/seurat-integrate:latest"
shell:
"Rscript Scripts/IntegrateSome.R "
"{input.data} "
"{input.tfval} "
"&> {log} "
rule PerformanceTesting:
input:
int1 = "data/svmtest1.h5ad",
int2 = "data/svmtest2.h5ad",
int3 = "data/svmtest3.h5ad",
int4 = "data/svmtest4.h5ad",
int5 = "data/svmtest5.h5ad"
output:
ukdf = "confusion/ukdf.csv",
data1 = "confusion/SVC/Lake_SVC_confusion.csv",
data2 = "confusion/SVC/Liao_SVC_confusion.csv",
data3 = "confusion/SVC/Menon_SVC_confusion.csv",
data4 = "confusion/SVC/Young_SVC_confusion.csv",
data5 = "confusion/SVC/Wu_SVC_confusion.csv",
data6 = "confusion/RandomForest/Lake_RandomForest_confusion.csv",
data7 = "confusion/RandomForest/Liao_RandomForest_confusion.csv",
data8 = "confusion/RandomForest/Menon_RandomForest_confusion.csv",
data9 = "confusion/RandomForest/Young_RandomForest_confusion.csv",
data10 = "confusion/RandomForest/Wu_RandomForest_confusion.csv",
data11 = "confusion/MLP/Lake_MLP_confusion.csv",
data12 = "confusion/MLP/Liao_MLP_confusion.csv",
data13 = "confusion/MLP/Menon_MLP_confusion.csv",
data14 = "confusion/MLP/Young_MLP_confusion.csv",
data15 = "confusion/MLP/Wu_MLP_confusion.csv",
data16 = "confusion/KNeighbor/Lake_KNeighbor_confusion.csv",
data17 = "confusion/KNeighbor/Liao_KNeighbor_confusion.csv",
data18 = "confusion/KNeighbor/Menon_KNeighbor_confusion.csv",
data19 = "confusion/KNeighbor/Young_KNeighbor_confusion.csv",
data20 = "confusion/KNeighbor/Wu_KNeighbor_confusion.csv",
data21 = "confusion/XGB/Lake_XGB_confusion.csv",
data22 = "confusion/XGB/Liao_XGB_confusion.csv",
data23 = "confusion/XGB/Menon_XGB_confusion.csv",
data24 = "confusion/XGB/Young_XGB_confusion.csv",
data25 = "confusion/XGB/Wu_XGB_confusion.csv",
medf1 = "scores/Median_F1_heatmap.pdf",
unkn = "confusion/Percent_Unknown_heatmap.pdf",
f1 = "scores/F1_scores.csv"
log: "data/PerformanceTesting.log"
singularity: "docker://sblough18/svm:latest"
shell:
"python3 Scripts/PerformanceTesting.py "
"{input.int1} "
"{input.int2} "
"{input.int3} "
"{input.int4} "
"{input.int5} "
"&> {log}"