-
Notifications
You must be signed in to change notification settings - Fork 0
/
Snakefile
184 lines (163 loc) · 7.42 KB
/
Snakefile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
#############################################################
# Snakefile for single cell analysis workflow
# P. RIVAUD
# 2020/04
#############################################################
import os
import re
import sys
sys.path.append("SCRIPTS")
from sample_list_extraction import sle, check_samples
from define_snakefile_targets import dst
from snakemake.logging import logger
######################################
# CONFIG FILE
######################################
configfile: "config.yaml" # load config file
######################################
# PATHS
######################################
OUTDIR=os.path.join(config['OUTDIR'],'') # grab folder information
INDIVDIR=os.path.join(config['INDIVDIR'],'')
######################################
# TARGETS
######################################
# steps that should be computed automatically:
# - step1_create_sce_obj
# - step2_cell_outliers
# - step4_gene_filtering
# - step5_doublet_filter
targets = dst(config, OUTDIR) # Define Snakefile Targets
rule all:
input: targets
######################################
# SAMPLE LIST EXTRACTION
######################################
SAMPLES = sle(config['AGGRFILE'], config['SAMPLE_EXTRACTION_FROMCOL'])
check_samples(SAMPLES, config['INDIVDIR'])
######################################
# PREPROCESSING
######################################
rule step1_create_sce_obj:
input:
aggrmatrix=config['AGGRMATRIX']
output:
rds_sce=OUTDIR+"objects/sce/sce.rds",
step_complete=OUTDIR+".completion/step1_create_sce_obj"
params:
outdir=OUTDIR,
ribogenesfile=config['RIBOGENESFILE']
script:
"SCRIPTS/step1_create_sce_obj.R"
rule step2_cell_outliers:
input:
rds_sce=OUTDIR+"objects/sce/sce.rds"
output:
rds_sce_cells=OUTDIR+"objects/sce/sce_cells.rds",
outliers_plot=OUTDIR+"QC/cell_outliers/QC_outlier_cells.pdf",
step_complete=OUTDIR+".completion/step2_cell_outliers"
script:
"SCRIPTS/step2_cell_outliers.R"
rule step3_cell_phase_assignment:
input:
rds_sce_cells=OUTDIR+"objects/sce/sce_cells.rds"
output:
rds_cell_phase=OUTDIR+"objects/cell_phase/cell_phase_assignments.rds",
cell_cycle_plot=OUTDIR+"QC/cell_cycle/QC_CellCycleAssignment.pdf",
cell_cycle_plot_colored=OUTDIR+"QC/cell_cycle/QC_CellCycleAssignment_colored.pdf",
step_complete=OUTDIR+".completion/step3_cell_phase_assignment"
script:
"SCRIPTS/step3_cell_phase_assignment.R"
rule step4_gene_filtering:
input:
rds_sce=OUTDIR+"objects/sce/sce.rds",
rds_sce_cells=OUTDIR+"objects/sce/sce_cells.rds"
output:
QC_genes_AveCounts_PCAOutliersRemoved=OUTDIR+"QC/genes/QC_genes_AveCounts_PCAOutliersRemoved.pdf",
QC_genes_NumCells_Counts_PCAOutliersRemoved=OUTDIR+"QC/genes/QC_genes_NumCells_Counts_PCAOutliersRemoved.pdf",
QC_genes_AveGeneExpr_breaks100=OUTDIR+'QC/genes/QC_genes_AveGeneExpr_breaks100.pdf',
QC_genes_AveGeneExpr_PCAOutliersRemoved_breaks100=OUTDIR+'QC/genes/QC_genes_AveGeneExpr_PCAOutliersRemoved_breaks100.pdf',
QC_genes_AveGeneExpr_PCAOutliersRemoved_LowAbundanceGenesRemoved_breaks100=OUTDIR+'QC/genes/QC_genes_AveGeneExpr_QcCellsGenes_breaks100.pdf',
QC_genes_Top50Expr_GreyHist_QcCellsGenes=OUTDIR+'QC/genes/QC_genes_Top50Expr_GreyHist_QcCellsGenes.pdf',
rds_sce_cells_genes=OUTDIR+"objects/sce/sce_cells_genes.rds",
step_complete=OUTDIR+".completion/step4_gene_filtering"
script:
"SCRIPTS/step4_gene_filtering.R"
rule step5_doublet_detection:
input:
rds_sce_cells_genes=OUTDIR+"objects/sce/sce_cells_genes.rds",
bcsfile=INDIVDIR+"{sample}/outs/filtered_feature_bc_matrix/barcodes.tsv.gz"
params:
samplelist=SAMPLES,
current_sample="{sample}"
output:
doublets_sample_file=OUTDIR+'DoubletFinder/barcode_lists/{sample}_barcodes_doublets.txt',
singlets_sample_file=OUTDIR+'DoubletFinder/barcode_lists/{sample}_barcodes_singlets.txt',
step_complete=OUTDIR+".completion/doubletfinder/{sample}"
script:
"SCRIPTS/step5_doublet_detection.R"
rule step5_doublet_filter:
input:
bcs_file_list=expand(OUTDIR+"DoubletFinder/barcode_lists/{sample}_barcodes_singlets.txt",sample=SAMPLES),
rds_sce_cells_genes=OUTDIR+"objects/sce/sce_cells_genes.rds",
output:
rds_sce_cells_genes_singlets=OUTDIR+"objects/sce/sce_cells_genes_singlets.rds",
rds_sce_cells_genes_DF=OUTDIR+"objects/sce/sce_cells_genes_DF.rds",
all_singlets=OUTDIR+'DoubletFinder/barcode_lists/ALL_barcodes_singlets.txt',
step_complete=OUTDIR+".completion/step5_doublet_filter"
script:
"SCRIPTS/step5_doublet_filter.R"
rule step6_norm_scran_deconvolution:
input:
rds_sce_cells_genes_singlets=OUTDIR+"objects/sce/sce_cells_genes_singlets.rds",
output:
rds_clusters=OUTDIR+"normalization/scran_deconvolution/ALL_normalization_clusters.rds",
plot_Norm_HistSizeFactors=OUTDIR+"normalization/scran_deconvolution/Norm_HistSizeFactors.pdf",
plot_Norm_SizeFactorsVsTotalCountsPerMillion=OUTDIR+"normalization/scran_deconvolution/Norm_SizeFactorsVsTotalCountsPerMillion.pdf",
plot_Norm_SizeFactorsVsTotalCounts_smooth=OUTDIR+"normalization/scran_deconvolution/Norm_SizeFactorsVsTotalCounts_smooth.pdf",
rds_sce_cells_genes_singlets_normed=OUTDIR+"objects/sce/sce_cells_genes_singlets_scran_deconvolution.rds",
step_complete=OUTDIR+".completion/step6_scran_deconvolution"
params:
individual_samples=0
script:
"SCRIPTS/step6_norm_scran_deconvolution.R"
rule step6_norm_scran_deconvolution_individual:
input:
sample_singlets=OUTDIR+"DoubletFinder/barcode_lists/{sample}_barcodes_singlets.txt",
rds_sce_cells_genes_singlets=OUTDIR+"objects/sce/sce_cells_genes_singlets.rds",
output:
rds_clusters=OUTDIR+"normalization/scran_deconvolution/individual_samples/{sample}/normalization_clusters.rds",
plot_Norm_HistSizeFactors=OUTDIR+"normalization/scran_deconvolution/individual_samples/{sample}/Norm_HistSizeFactors.pdf",
plot_Norm_SizeFactorsVsTotalCountsPerMillion=OUTDIR+"normalization/scran_deconvolution/individual_samples/{sample}/Norm_SizeFactorsVsTotalCountsPerMillion.pdf",
plot_Norm_SizeFactorsVsTotalCounts_smooth=OUTDIR+"normalization/scran_deconvolution/individual_samples/{sample}/Norm_SizeFactorsVsTotalCounts_smooth.pdf",
rds_sce_cells_genes_singlets_normed=OUTDIR+"objects/sce/individual_samples/{sample}/sce_cells_genes_singlets_scran_deconvolution.rds",
step_complete=OUTDIR+".completion/individual_normalization/step6_scran_deconvolution_{sample}"
params:
individual_samples=1
script:
"SCRIPTS/step6_norm_scran_deconvolution.R"
rule step6_merge_individual_scran_deconvolutions:
input:
individual_files=expand(OUTDIR+"objects/sce/individual_samples/{sample}/sce_cells_genes_singlets_scran_deconvolution.rds", sample=SAMPLES)
output:
rds_sce_cells_genes_singlets_scran_deconvolution_merged=OUTDIR+"objects/sce/sce_cells_genes_singlets_scran_deconvolution_merged.rds",
step_complete=OUTDIR+".completion/step6_scran_deconvolution_merged"
script:
"SCRIPTS/step6_merge_individual_scran_deconvolutions.R"
rule step6_seurat_sctransform:
input:
rds_sce_cells_genes_singlets=OUTDIR+"objects/sce/sce_cells_genes_singlets.rds"
output:
seurat_cells_genes_singlets_normed=OUTDIR+"objects/seurat/seurat_cells_genes_singlets_seurat_sctransform.rds",
plot_umap=OUTDIR+'normalization/seurat_sctransform/umap_normed.pdf',
step_complete=OUTDIR+".completion/step6_seurat_sctransform"
script:
"SCRIPTS/step6_norm_seurat_sctransform.R"
rule seurat3_pipe:
input:
rds_sce_cells_genes_singlets=OUTDIR+"objects/sce/sce_cells_genes_singlets.rds"
output:
rds_seurat=OUTDIR+'objects/seurat/seurat_pipe.rds',
step_complete=OUTDIR+".completion/step_seurat3_pipe"
script:
"SCRIPTS/step_seurat3_pipe.R"