diff --git a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/config.yaml b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/config.yaml index 7c7164a9..74f13ec5 100644 --- a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/config.yaml +++ b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/config.yaml @@ -4,10 +4,7 @@ method_list: [lofreq_local_haplo, cliquesnv_local_haplo_snv, cliquesnv_local_haplo_tf0.01, cliquesnv_local_haplo_snv_tf0.01, - viloca, - viloca_envp, - viloca_multi, - viloca_envp_multi, + viloca_alpha_0.000001, shorah_default_amplicon, ] replicate_count: 5 diff --git a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/params.csv b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/params.csv index 0190d3f2..492c4da9 100644 --- a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/params.csv +++ b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/params.csv @@ -1,57 +1,41 @@ seq_tech,seq_mode,seq_mode_param,read_length,genome_size,coverage,haplos -# -# Population 1 -- Illumina -illumina,shotgun,single_amplicon,249,249,100,5@5@20@4@12@geom@0.75 -illumina,shotgun,single_amplicon,249,249,200,5@5@20@4@12@geom@0.75 -illumina,shotgun,single_amplicon,249,249,500,5@5@20@4@12@geom@0.75 -illumina,shotgun,single_amplicon,249,249,800,5@5@20@4@12@geom@0.75 +# Population 1 +illumina,shotgun,single_amplicon,249,249,1000,2@3@30@20@20@geom@0.75 +# Population 2 illumina,shotgun,single_amplicon,249,249,1000,5@5@20@4@12@geom@0.75 -illumina,shotgun,single_amplicon,249,249,5000,5@5@20@4@12@geom@0.75 -illumina,shotgun,single_amplicon,249,249,10000,5@5@20@4@12@geom@0.75 -# -# Population 2 -- Illumina -illumina,shotgun,single_amplicon,249,249,100,5@10@30@10@10@geom@0.75 -illumina,shotgun,single_amplicon,249,249,200,5@10@30@10@10@geom@0.75 -illumina,shotgun,single_amplicon,249,249,500,5@10@30@10@10@geom@0.75 -illumina,shotgun,single_amplicon,249,249,800,5@10@30@10@10@geom@0.75 -illumina,shotgun,single_amplicon,249,249,1000,5@10@30@10@10@geom@0.75 -illumina,shotgun,single_amplicon,249,249,5000,5@10@30@10@10@geom@0.75 -illumina,shotgun,single_amplicon,249,249,10000,5@10@30@10@10@geom@0.75 -# -# Population 3 -- Illumina -illumina,shotgun,single_amplicon,249,249,100,5@3@30@20@20@geom@0.75 -illumina,shotgun,single_amplicon,249,249,200,5@3@30@20@20@geom@0.75 -illumina,shotgun,single_amplicon,249,249,500,5@3@30@20@20@geom@0.75 -illumina,shotgun,single_amplicon,249,249,800,5@3@30@20@20@geom@0.75 -illumina,shotgun,single_amplicon,249,249,1000,5@3@30@20@20@geom@0.75 -illumina,shotgun,single_amplicon,249,249,5000,5@3@30@20@20@geom@0.75 -illumina,shotgun,single_amplicon,249,249,10000,5@3@30@20@20@geom@0.75 -# -# Population 4-- Illumina -illumina,shotgun,single_amplicon,249,249,100,10@15@30@20@20@geom@0.75 -illumina,shotgun,single_amplicon,249,249,200,10@15@30@20@20@geom@0.75 -illumina,shotgun,single_amplicon,249,249,500,10@15@30@20@20@geom@0.75 -illumina,shotgun,single_amplicon,249,249,800,10@15@30@20@20@geom@0.75 -illumina,shotgun,single_amplicon,249,249,1000,10@15@30@20@20@geom@0.75 -illumina,shotgun,single_amplicon,249,249,5000,10@15@30@20@20@geom@0.75 -illumina,shotgun,single_amplicon,249,249,10000,10@15@30@20@20@geom@0.75 -# -# long reads -- population 1 -nanopore,shotgun,single_amplicon,5000,5000,1000,2@3@240@40@120@geom@0.75 -pacbio,shotgun,single_amplicon,5000,5000,1000,2@3@240@40@120@geom@0.75 -# -# long reads -- population 2 -nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@240@40@120@geom@0.75 -pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@240@40@120@geom@0.75 -# -# long reads -- population 3 -nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@240@40@120@geom@0.75 -pacbio,shotgun,single_amplicon,5000,5000,1000,5@10@240@40@120@geom@0.75 -# -# long reads -- population 4 -nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@200@geom@0.75 -pacbio,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@200@geom@0.75 -# -# long reads -- population 5 -nanopore,shotgun,single_amplicon,5000,5000,1000,15@5@600@200@200@geom@0.75 -pacbio,shotgun,single_amplicon,5000,5000,1000,15@5@600@200@200@geom@0.75 +# Population 3 (vary covverage) +illumina,shotgun,single_amplicon,249,249,100,5@5@30@10@15@geom@0.75 +illumina,shotgun,single_amplicon,249,249,500,5@5@30@10@15@geom@0.75 +illumina,shotgun,single_amplicon,249,249,800,5@5@30@10@15@geom@0.75 +illumina,shotgun,single_amplicon,249,249,1000,5@5@30@10@15@geom@0.75 +illumina,shotgun,single_amplicon,249,249,5000,5@5@30@10@15@geom@0.75 +illumina,shotgun,single_amplicon,249,249,10000,5@5@30@10@15@geom@0.75 +# Population 4 +illumina,shotgun,single_amplicon,249,249,1000,5@10@30@10@15@geom@0.75 +# Population 5 +illumina,shotgun,single_amplicon,249,249,1000,5@15@30@10@15@geom@0.75 +# Population 6 +nanopore,shotgun,single_amplicon,5000,5000,1000,2@3@600@400@400@geom@0.75 +pacbio,shotgun,single_amplicon,5000,5000,1000,2@3@600@400@400@geom@0.75 +# Population 7 +nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@240@geom@0.75 +pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@240@geom@0.75 +# Population 8 (vary coverage) +nanopore,shotgun,single_amplicon,5000,5000,100,5@5@600@200@300@geom@0.75 +nanopore,shotgun,single_amplicon,5000,5000,200,5@5@600@200@300@geom@0.75 +nanopore,shotgun,single_amplicon,5000,5000,500,5@5@600@200@300@geom@0.75 +nanopore,shotgun,single_amplicon,5000,5000,800,5@5@600@200@300@geom@0.75 +nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@300@geom@0.75 +nanopore,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@300@geom@0.75 +pacbio,shotgun,single_amplicon,5000,5000,100,5@5@600@200@300@geom@0.75 +pacbio,shotgun,single_amplicon,5000,5000,200,5@5@600@200@300@geom@0.75 +pacbio,shotgun,single_amplicon,5000,5000,500,5@5@600@200@300@geom@0.75 +pacbio,shotgun,single_amplicon,5000,5000,800,5@5@600@200@300@geom@0.75 +pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@300@geom@0.75 +pacbio,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@300@geom@0.75 +# Population 9 +nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@300@geom@0.75 +pacbio,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@300@geom@0.75 +# Population 10 +nanopore,shotgun,single_amplicon,5000,5000,1000,15@5@600@300@200@geom@0.75 +pacbio,shotgun,single_amplicon,5000,5000,1000,15@5@600@300@200@geom@0.75 diff --git a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_realdata/config.yaml b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_realdata/config.yaml index f48f82c1..caa40f2b 100644 --- a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_realdata/config.yaml +++ b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_realdata/config.yaml @@ -4,7 +4,7 @@ method_list: [lofreq_local_haplo, cliquesnv_local_haplo_snv, cliquesnv_local_haplo_tf0.01, cliquesnv_local_haplo_snv_tf0.01, - viloca, + viloca_alpha_0.000001, ] replicate_count: 1 haplotype_generation: null diff --git a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_realdata/params.csv b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_realdata/params.csv index d1f73b7c..32520e49 100644 --- a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_realdata/params.csv +++ b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_realdata/params.csv @@ -2,20 +2,19 @@ seq_tech,seq_mode,seq_mode_param,read_length,genome_size,coverage,haplos # # HIV-5-Virus-Mix illumina,real_data,5-virus-mix,,,1, -#illumina,real_data,5-virus-mix,,,0.75, # # PVY-5-Strain-Mix nanopore,amplicon,real_data,Five_strain_PVY,,9698, -# PVY-5-Strain-Mix +# IAV- 10 strain mix pacbio,amplicon,real_data,Ten_strain_IAV,,2300, # # Two-Strain-SARS-CoV-2 illumina,amplicon,real_data,Two-strain-SARS-CoV-2,G1_Wild_100_01,1, illumina,amplicon,real_data,Two-strain-SARS-CoV-2,H1_Wild_100_02,1, illumina,amplicon,real_data,Two-strain-SARS-CoV-2,D1_Wild_50_01,1, -illumina,amplicon,real_data,Two-strain-SARS-CoV-2,D3_Wild_50_04,1, +#illumina,amplicon,real_data,Two-strain-SARS-CoV-2,D3_Wild_50_04,1, illumina,amplicon,real_data,Two-strain-SARS-CoV-2,E1_Wild_50_02,1, -illumina,amplicon,real_data,Two-strain-SARS-CoV-2,A3_Wild_10_04,1, -illumina,amplicon,real_data,Two-strain-SARS-CoV-2,B1_Wild_10_02,1, +#illumina,amplicon,real_data,Two-strain-SARS-CoV-2,A3_Wild_10_04,1, +#illumina,amplicon,real_data,Two-strain-SARS-CoV-2,B1_Wild_10_02,1, illumina,amplicon,real_data,Two-strain-SARS-CoV-2,C2_Wild_10_03,1, -illumina,amplicon,real_data,Two-strain-SARS-CoV-2,G2_Wild_100_03,1, +#illumina,amplicon,real_data,Two-strain-SARS-CoV-2,G2_Wild_100_03,1, diff --git a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/workflow/Snakefile b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/workflow/Snakefile index 163f627f..746e81c5 100644 --- a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/workflow/Snakefile +++ b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/workflow/Snakefile @@ -69,7 +69,7 @@ use rule run_method_local from varyvilocaparams as varyvilocaparams_run_method_l f"results/varyvilocaparams/method_runs/{varyvilocaparams.paramspace.wildcard_pattern}/{{method,{'|'.join(['markertoavoidemptyregex'] + varyvilocaparams.method_list)}}}/replicates/{{replicate}}/benchmark_.tsv" resources: mem_mb=20024, - runtime=4, + runtime=240, threads=10, @@ -176,8 +176,9 @@ use rule run_method_local from distance as distance_run_method_local_global with benchmark: f"results/distance/method_runs/{distance.paramspace.wildcard_pattern}/{{method,{'|'.join(['markertoavoidemptyregex'] + distance.method_list)}}}/replicates/{{replicate}}/benchmark_.tsv" resources: - mem_mb=8024, - runtime=8000, + mem_mb=20024, + runtime=14400, + threads=25 use rule performance_measures_local from distance as distance_performance_measures_local with: @@ -260,9 +261,9 @@ use rule run_method_local from realdata as realdata_run_method_local_global with benchmark: f"results/realdata/method_runs/{realdata.paramspace.wildcard_pattern}/{{method,{'|'.join(['markertoavoidemptyregex'] + realdata.method_list)}}}/replicates/{{replicate}}/benchmark_.tsv" resources: - mem_mb=18024, + mem_mb=60024, runtime=16000, - threads=120, + threads=30, use rule performance_measures_local from realdata as realdata_performance_measures_local with: