fixup: alignment params

nextstrain · Jan 31, 2024 · 2dce01b · 2dce01b
1 parent 544e877
commit 2dce01b
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Showing 5 changed files with 9 additions and 5 deletions.
diff --git a/ingest/workflow/snakemake_rules/nextclade.smk b/ingest/workflow/snakemake_rules/nextclade.smk
@@ -82,7 +82,7 @@ rule nextclade_denvX:
         "data/nextclade_results/nextclade_denv{x}.tsv",
     threads: 4
     params:
-        min_seed_cover=0.01,
+        min_seed_cover=0.1,
     shell:
         """
         nextclade run \

diff --git a/nextclade_data/denv1/pathogen.json b/nextclade_data/denv1/pathogen.json
@@ -1,6 +1,7 @@
 {
   "alignmentParams": {
-    "minSeedCover": 0.01
+    "minSeedCover": 0.1,
+    "minLength": 1000
   },
   "attributes": {
     "name": "Dengue virus DENV1 dataset",

diff --git a/nextclade_data/denv2/pathogen.json b/nextclade_data/denv2/pathogen.json
@@ -1,6 +1,7 @@
 {
   "alignmentParams": {
-    "minSeedCover": 0.01
+    "minSeedCover": 0.1,
+    "minLength": 1000
   },
   "attributes": {
     "name": "Dengue virus DENV2 dataset",

diff --git a/nextclade_data/denv3/pathogen.json b/nextclade_data/denv3/pathogen.json
@@ -1,6 +1,7 @@
 {
   "alignmentParams": {
-    "minSeedCover": 0.01
+    "minSeedCover": 0.1,
+    "minLength": 1000
   },
   "attributes": {
     "name": "Dengue virus DENV3 dataset",

diff --git a/nextclade_data/denv4/pathogen.json b/nextclade_data/denv4/pathogen.json
@@ -1,6 +1,7 @@
 {
   "alignmentParams": {
-    "minSeedCover": 0.01
+    "minSeedCover": 0.1,
+    "minLength": 1000
   },
   "attributes": {
     "name": "Dengue virus DENV4 dataset",