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graph.txt
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digraph G {
#snakemake -s Snakefile_UMI.smk --dag |tail -n+2 |dot -Tpng > dag.png
subgraph cluster_0 {
style=filled;
color=lightgrey;
node [style=filled,color=white];
a0 -> a1 -> a2 -> a3;
label = "process #1";
}
subgraph cluster_1 {
node [style=filled];
b0 -> b1 -> b2 -> b3;
label = "process #2";
color=blue
}
start -> a0;
start -> b0;
a1 -> b3;
b2 -> a3;
a3 -> a0;
a3 -> end;
b3 -> end;
subgraph cluster_3 {
node [style=filled];
4, 3, 2;
label = "pre-processing";
}
subgraph cluster_4 {
node [style=filled];
5, 1, 2 ,6;
label = "mapping";
}
subgraph cluster_5 {
node [style=filled];
16, 15;
label = "assembly";
}
subgraph cluster_6 {
node [style=filled];
11, 8, 10,12,9,13 ;
label = "UMI correction";
}
subgraph cluster_7 {
node [style=filled];
18, 19,20,7;
label = "UMI aware variant calling";
}
subgraph cluster_8 {
node [style=filled];
23 ;
label = "removing duplicates";
}
subgraph cluster_9 {
node [style=filled];
22, 24,25;
label = "UMI unaware variant calling";
}
graph[bgcolor=white, margin=0];
node[shape=box, style=rounded, fontname=sans, fontsize=10, penwidth=2];
edge[penwidth=2, color=grey];
#0[label = "all", color = "0.25 0.6 0.85", style="rounded"];
4[label = "add_barcode\ns: 21014a009_01", color = "0.11 0.6 0.85", style="rounded"];
3[label = "trimming", color = "0.23 0.6 0.85", style="rounded"];
1[label = "mapping", color = "0.28 0.6 0.85", style="rounded"];
2[label = "kraken", color = "0.37 0.6 0.85", style="rounded"];
5[label = "index_reference", color = "0.41 0.6 0.85", style="rounded"];
6[label = "cov_depth_qc", color = "0.21 0.6 0.85", style="rounded"];
7[label = "ivar", color = "0.16 0.6 0.85", style="rounded"];
8[label = "sort_by_position_overlap", color = "0.53 0.6 0.85", style="rounded"];
9[label = "bamclipoverlap", color = "0.07 0.6 0.85", style="rounded"];
10[label = "sort_by_position_after_correction", color = "0.51 0.6 0.85", style="rounded"];
11[label = "barcode_correction", color = "0.39 0.6 0.85", style="rounded"];
12[label = "index_after_correction", color = "0.30 0.6 0.85", style="rounded"];
13[label = "index_overlap", color = "0.02 0.6 0.85", style="rounded"];
14[label = "consensus_ivar", color = "0.05 0.6 0.85", style="rounded"];
15[label = "quast", color = "0.32 0.6 0.85", style="rounded"];
16[label = "assembly", color = "0.62 0.6 0.85", style="rounded"];
17[label = "ivar_variant_table", color = "0.34 0.6 0.85", style="rounded"];
18[label = "umivar2", color = "0.44 0.6 0.85", style="rounded"];
19[label = "lofreq_call", color = "0.48 0.6 0.85", style="rounded"];
20[label = "varscan", color = "0.00 0.6 0.85", style="rounded"];
21[label = "ivar_variant_table_ignore", color = "0.64 0.6 0.85", style="rounded"];
22[label = "ivar_ignore", color = "0.09 0.6 0.85", style="rounded"];
23[label = "mapping_duplicate_samblaster", color = "0.57 0.6 0.85", style="rounded"];
24[label = "lofreq_call_ignore", color = "0.55 0.6 0.85", style="rounded"];
25[label = "varscan_ignore", color = "0.14 0.6 0.85", style="rounded"];
s="SampleID"
26[label="krakendb"]; # krakendb
26 ->2
27[label="reference"]; # reference genome
27->5
28[label="Sample_{s}/{s}.viral.bam"]; # mapping
29[label="Sample_{s}/coverage/{s}.mosdepth.summary.txt"]; # coverage depth qc
/* expand('Sample_{s}/ivar/{s}_ivar.vcf.gz', s = all_sampleids), # variant calling
expand('Sample_{s}/consensus/{s}_consensus_ivar.fa', s = all_sampleids), # consensus ivar
#expand('Sample_{s}/consensus/{s}_umivar.fasta', s = all_sampleids), # consensus umivar
expand('Sample_{s}/quast_results', s = all_sampleids), # assembly
expand('Sample_{s}/ivar/{s}.variants.txt', s = all_sampleids), # variants.txt
#expand('Sample_{s}/umivar2/{s}.viral_hq.vcf', s = all_sampleids), #umiVar2
expand('Sample_{s}/umivar2/{s}_bamclipoverlap_sorted_hq.vcf', s = all_sampleids), #umiVar2
expand('Sample_{s}/lofreq/{s}_lofreq.tsv', s = all_sampleids), # Lofreq
expand('Sample_{s}/varscan/{s}_varscan.tsv', s = all_sampleids), # varscan
expand('Sample_{s}/dedup/ivar/{s}.variants.txt', s = all_sampleids), # variants.txt
expand('Sample_{s}/dedup/lofreq/{s}_lofreq.tsv', s = all_sampleids), # Lofreq
expand('Sample_{s}/dedup/varscan/{s}_varscan.tsv', s = all_sampleids), # varscan
expand('Sample_{s}/{s}_R1_trimmed.fastq.gz', s = all_sampleids)#want to check output */
# 1 -> 0
# 6 -> 0
# 7 -> 0
# 14 -> 0
# 15 -> 0
# 17 -> 0
# 18 -> 0
# 19 -> 0
# 20 -> 0
# 21 -> 0
# 24 -> 0
# 25 -> 0
# 3 -> 0
2 -> 1
5 -> 1
3 -> 2
4 -> 3
1 -> 6
8 -> 7
13 -> 7
9 -> 8
10 -> 9
12 -> 9
11 -> 10
1 -> 11
10 -> 12
8 -> 13
1 -> 14
16 -> 15
2 -> 16
7 -> 17
8 -> 18
8 -> 19
8 -> 20
22 -> 21
23 -> 22
1 -> 23
23 -> 24
23 -> 25
21 -> table;
start [shape=Mdiamond];
end [shape=Msquare];
}