extend simulation scenarios and methods list

cbg-ethz · Sep 6, 2024 · dd6fd24 · dd6fd24
1 parent 7ebdc8f
commit dd6fd24
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diff --git a/...auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/config.yaml b/...auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/config.yaml
@@ -5,6 +5,8 @@ method_list: [lofreq_local_haplo,
               cliquesnv_local_haplo_tf0.1,
               cliquesnv_local_haplo_tf0.01,
               viloca_alpha_0.00001,
+              haploflow,
+              haplodmf,
               #strainline,  failed in clustering step
               # shorah_default_amplicon, --> here the short illumina simulation still not work due to b2w errors
               ]

diff --git a/.../auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/params.csv b/.../auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/params.csv
@@ -37,3 +37,9 @@ pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@300@[email protected]
 # Population 8
 nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@240@[email protected]
 pacbio,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@240@[email protected]
+# revisions
+# Population 10
+pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@100@5@5@[email protected]
+nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@100@5@5@[email protected]
+# Population 5
+illumina,shotgun,single_amplicon,249,249,1000,10@5@5@4@3@[email protected]
diff --git a/...auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_realdata/config.yaml b/...auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_realdata/config.yaml
@@ -3,6 +3,7 @@ method_list: [lofreq_local_haplo,
               predicthaplo_local_haplo,
               viloca_alpha_0.00001,
               cliquesnv_local_haplo_tf0.001,
+              haplodmf,
               ]
 replicate_count: 1
 haplotype_generation: null