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+
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+
+
+
+153->159
+
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+
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+
+
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+
+
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+
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+
+
+
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+
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+
+
+
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+
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+
+
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+
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+
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+
+
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+
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+
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+nv_panel_zoom_on_feature_data
+region_name: S
+
+
+
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+
+
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+
+
+
+162->160
+
+
+
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+region_name: S
+
+
+
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+
+
+
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+
+
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+
+
+
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+
+
+
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+
+
+
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+
+
+
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+
+
+
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+
+
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+
+
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+
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+
+
+
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+
+
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+
+
+
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+
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+
+
+
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+
+
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+172->171
+
+
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+pairwise_trajectory_correlation_data
+
+
+
+172->213
+
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+
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+
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+
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+filter_mpileup_all_sites
+
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+
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+188->206
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+189->188
+
+
+
+190
+filter_mpileup_all_sites
+
+
+
+190->173
+
+
+
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+
+
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+191->190
+
+
+
+192
+filter_mpileup_all_sites
+
+
+
+192->173
+
+
+
+192->206
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+
+
+193->192
+
+
+
+194
+filter_mpileup_all_sites
+
+
+
+194->173
+
+
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+
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+195->194
+
+
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+196
+filter_mpileup_all_sites
+
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+198->1
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+199->1
+
+
+
+200
+allele_freq_tree_data
+
+
+
+200->199
+
+
+
+208
+time_signal_data
+
+
+
+200->208
+
+
+
+201
+format_afwdist_results
+
+
+
+201->200
+
+
+
+202->201
+
+
+
+203->202
+
+
+
+204->203
+
+
+
+205
+compile_fail_sites_vcf
+
+
+
+205->204
+
+
+
+206->205
+
+
+
+207
+time_signal_plot
+
+
+
+207->1
+
+
+
+208->1
+
+
+
+208->207
+
+
+
+209
+dnds_plots
+
+
+
+209->1
+
+
+
+210->209
+
+
+
+211->210
+
+
+
+212->210
+
+
+
+212->211
+
+
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+213->1
+
+
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+214->1
+
+
+
+215->1
+
+
+
diff --git a/.rulegraph.png b/.rulegraph.png
deleted file mode 100644
index d3bcf3c..0000000
Binary files a/.rulegraph.png and /dev/null differ
diff --git a/.rulegraph.svg b/.rulegraph.svg
new file mode 100644
index 0000000..114780a
--- /dev/null
+++ b/.rulegraph.svg
@@ -0,0 +1,1153 @@
+
+
+
+
+
+
+snakemake_dag
+
+0
+all
+
+
+
+1
+report
+
+
+
+1->0
+
+
+
+2
+demix_plot
+
+
+
+2->1
+
+
+
+3
+demix_plot_data
+
+
+
+3->2
+
+
+
+4
+summarise_demix
+
+
+
+4->3
+
+
+
+5
+demix
+
+
+
+5->4
+
+
+
+6
+demix_preprocessing
+
+
+
+6->5
+
+
+
+7
+fetch_mapping_references
+
+
+
+7->6
+
+
+
+8
+read_bam_refs
+
+
+
+8->7
+
+
+
+9
+demix_barcode_update
+
+
+
+9->1
+
+
+
+9->5
+
+
+
+10
+context_phylogeny_plot
+
+
+
+10->1
+
+
+
+11
+ml_context_tree
+
+
+
+11->10
+
+
+
+22
+context_phylogeny_data
+
+
+
+11->22
+
+
+
+12
+mask_alignment
+
+
+
+12->11
+
+
+
+24
+diversity_data
+
+
+
+12->24
+
+
+
+33
+reconstruct_ancestral_sequence
+
+
+
+12->33
+
+
+
+13
+align_fasta
+
+
+
+13->12
+
+
+
+14
+fetch_alignment_reference
+
+
+
+14->12
+
+
+
+14->13
+
+
+
+18
+mask_context
+
+
+
+14->18
+
+
+
+19
+align_context
+
+
+
+14->19
+
+
+
+60
+extract_afwdist_variants
+
+
+
+14->60
+
+
+
+15
+concat_fasta
+
+
+
+15->13
+
+
+
+21
+pangolin_report
+
+
+
+15->21
+
+
+
+15->22
+
+
+
+56
+allele_freq_tree_plot
+
+
+
+15->56
+
+
+
+16
+rename_fastas
+
+
+
+16->15
+
+
+
+17
+fetch_problematic_vcf
+
+
+
+17->12
+
+
+
+17->18
+
+
+
+30
+mask_tsv
+
+
+
+17->30
+
+
+
+61
+merge_mask_sites_vcf
+
+
+
+17->61
+
+
+
+69
+problematic_vcf_to_bed
+
+
+
+17->69
+
+
+
+18->11
+
+
+
+18->24
+
+
+
+19->18
+
+
+
+20
+download_context
+
+
+
+20->19
+
+
+
+21->20
+
+
+
+71
+summary_table
+
+
+
+21->71
+
+
+
+22->1
+
+
+
+22->10
+
+
+
+23
+diversity_plot
+
+
+
+23->1
+
+
+
+24->1
+
+
+
+24->23
+
+
+
+25
+polymorphic_sites_over_time_plot
+
+
+
+25->1
+
+
+
+26
+polymorphic_sites_over_time_data
+
+
+
+26->25
+
+
+
+72
+merge_json_files
+
+
+
+26->72
+
+
+
+27
+concat_variants
+
+
+
+27->26
+
+
+
+40
+nv_panel_data
+
+
+
+27->40
+
+
+
+41
+window_data
+
+
+
+27->41
+
+
+
+51
+fill_all_sites
+
+
+
+27->51
+
+
+
+27->60
+
+
+
+67
+calculate_dnds
+
+
+
+27->67
+
+
+
+28
+merge_annotation
+
+
+
+28->27
+
+
+
+29
+filter_tsv
+
+
+
+29->28
+
+
+
+38
+tsv_to_vcf
+
+
+
+29->38
+
+
+
+30->29
+
+
+
+31
+snps_to_ancestor
+
+
+
+31->30
+
+
+
+54
+bcftools_mpileup_all_sites
+
+
+
+31->54
+
+
+
+32
+ancestor_fasta
+
+
+
+32->31
+
+
+
+59
+afwdist_weighted_distances
+
+
+
+32->59
+
+
+
+32->60
+
+
+
+68
+n_s_sites
+
+
+
+32->68
+
+
+
+33->32
+
+
+
+34
+fetch_alignment_annotation
+
+
+
+34->31
+
+
+
+35
+format_vcf_fields_longer
+
+
+
+35->28
+
+
+
+36
+extract_vcf_fields
+
+
+
+36->35
+
+
+
+37
+variants_effect
+
+
+
+37->36
+
+
+
+38->37
+
+
+
+39
+nv_panel_plot
+
+
+
+39->1
+
+
+
+40->39
+
+
+
+46
+nv_panel_zoom_on_feature_data
+
+
+
+40->46
+
+
+
+40->72
+
+
+
+41->39
+
+
+
+47
+window_zoom_on_feature_data
+
+
+
+41->47
+
+
+
+41->72
+
+
+
+42
+fetch_reference_gb
+
+
+
+42->41
+
+
+
+44
+filter_genbank_features
+
+
+
+42->44
+
+
+
+43
+extract_genbank_regions
+
+
+
+43->39
+
+
+
+45
+nv_panel_plot_S
+
+
+
+43->45
+
+
+
+43->46
+
+
+
+43->47
+
+
+
+44->43
+
+
+
+44->68
+
+
+
+45->1
+
+
+
+46->45
+
+
+
+47->45
+
+
+
+48
+create_empty_file
+
+
+
+48->45
+
+
+
+49
+af_time_correlation_plot
+
+
+
+49->1
+
+
+
+50
+af_time_correlation_data
+
+
+
+50->49
+
+
+
+55
+af_trajectory_panel_plot
+
+
+
+50->55
+
+
+
+51->50
+
+
+
+70
+pairwise_trajectory_correlation_data
+
+
+
+51->70
+
+
+
+52
+merge_filtered_mpileup_all_sites
+
+
+
+52->51
+
+
+
+53
+filter_mpileup_all_sites
+
+
+
+53->52
+
+
+
+63
+merge_fail_mpileup_all_sites
+
+
+
+53->63
+
+
+
+54->53
+
+
+
+55->1
+
+
+
+56->1
+
+
+
+57
+allele_freq_tree_data
+
+
+
+57->56
+
+
+
+65
+time_signal_data
+
+
+
+57->65
+
+
+
+58
+format_afwdist_results
+
+
+
+58->57
+
+
+
+59->58
+
+
+
+60->59
+
+
+
+61->60
+
+
+
+62
+compile_fail_sites_vcf
+
+
+
+62->61
+
+
+
+63->62
+
+
+
+64
+time_signal_plot
+
+
+
+64->1
+
+
+
+65->1
+
+
+
+65->64
+
+
+
+66
+dnds_plots
+
+
+
+66->1
+
+
+
+67->66
+
+
+
+68->67
+
+
+
+69->67
+
+
+
+69->68
+
+
+
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+
+
+
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+
+
+
+72->1
+
+
+
diff --git a/.rulegraph_sv.svg b/.rulegraph_sv.svg
index d7ff0c7..b82d82f 100644
--- a/.rulegraph_sv.svg
+++ b/.rulegraph_sv.svg
@@ -1 +1 @@
-read_bam_refs demix_barcode_update fetch_alignment_reference rename_fastas fetch_problematic_vcf fetch_alignment_annotation fetch_reference_gb create_empty_file fetch_mapping_references concat_fasta filter_genbank_features demix_preprocessing align_fasta pangolin_report extract_genbank_regions demix mask_alignment download_context summary_table summarise_demix reconstruct_ancestral_sequence align_context demix_plot_data ancestor_fasta mask_context demix_plot snps_to_ancestor n_s_sites ml_context_tree diversity_data mask_tsv context_phylogeny_data diversity_plot filter_tsv context_phylogeny_plot tsv_to_vcf variants_effect extract_vcf_fields format_vcf_fields_longer merge_annotation concat_variants polymorphic_sites_over_time_data nv_panel_data window_data af_time_correlation_data extract_afwdist_variants calculate_dnds pairwise_trajectory_correlation polymorphic_sites_over_time_plot nv_panel_zoom_on_feature_data nv_panel_plot window_zoom_on_feature_data merge_json_files af_time_correlation_plot af_trajectory_panel_plot afwdist_weighted_distances dnds_plots nv_panel_plot_S format_afwdist_results allele_freq_tree_data allele_freq_tree_plot time_signal_data time_signal_plot report read_bam_refs demix_barcode_update fetch_alignment_reference rename_fastas fetch_problematic_vcf fetch_alignment_annotation fetch_reference_gb create_empty_file fetch_mapping_references concat_fasta problematic_vcf_to_bed filter_genbank_features demix_preprocessing align_fasta pangolin_report extract_genbank_regions demix mask_alignment download_context summary_table summarise_demix reconstruct_ancestral_sequence align_context demix_plot_data ancestor_fasta mask_context demix_plot snps_to_ancestor n_s_sites ml_context_tree diversity_data mask_tsv bcftools_mpileup_all_sites context_phylogeny_data diversity_plot filter_tsv filter_mpileup_all_sites context_phylogeny_plot tsv_to_vcf merge_filtered_mpileup_all_sites merge_fail_mpileup_all_sites variants_effect compile_fail_sites_vcf extract_vcf_fields merge_mask_sites_vcf format_vcf_fields_longer merge_annotation concat_variants polymorphic_sites_over_time_data nv_panel_data window_data fill_all_sites extract_afwdist_variants calculate_dnds polymorphic_sites_over_time_plot nv_panel_zoom_on_feature_data nv_panel_plot window_zoom_on_feature_data merge_json_files af_time_correlation_data pairwise_trajectory_correlation_data afwdist_weighted_distances dnds_plots nv_panel_plot_S af_time_correlation_plot af_trajectory_panel_plot format_afwdist_results allele_freq_tree_data allele_freq_tree_plot time_signal_data time_signal_plot report
+Rule graph image
+
+
+
+
The same graph can also be rendered with other tools such as [snakevision](https://github.com/OpenOmics/snakevision) (v0.1.0).
@@ -218,15 +223,25 @@ The same graph can also be rendered with other tools such as [snakevision](https
snakemake --forceall --rulegraph | snakevision -s all -o .rulegraph_sv.svg
```
+
+Snakevision rule graph image
+
-The `--dag` option emits an directed acyclic graph (DAG) that corresponds to the rule instances that would be executed for the current dataset. The example below produces an image using Graphviz:
+
+
+The `--dag` option emits an directed acyclic graph (DAG) that corresponds to the rule instances that would be executed for the target dataset. The example below produces an image using Graphviz (for [data](https://doi.org/10.20350/digitalCSIC/15648) from [our study](https://doi.org/10.1093/ve/veae018)):
```shell
-snakemake --forceall --dag | dot -Tpng >.dag.png
+snakemake --forceall --dag | dot -Grankdir=LR -Tsvg >.dag.svg
```
-
+
+DAG image
+
+
+
+
## Run modes