profiles/upload: Add prioritized_seqs_file to config

Follow workflows current set up to provide file paths with the `{segment}` wildcard in the config. Includes skeleton files for all segments of h1n1pdm, h3n2, and vic that can be filled in as we define prioritized sequences.
nextstrain · Jan 22, 2025 · 4eb8334 · 4eb8334
1 parent e84038a
commit 4eb8334
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diff --git a/profiles/upload.yaml b/profiles/upload.yaml
@@ -74,6 +74,7 @@ recency:
 builds:
   h1n1pdm_2y:
     lineage: h1n1pdm
+    prioritized_seqs_file: "profiles/upload/h1n1pdm/{segment}/prioritized_seqs_file.tsv"
     reference: "config/h1n1pdm/{segment}/reference.fasta"
     annotation: "config/h1n1pdm/{segment}/genemap.gff"
     tree_exclude_sites: "config/h1n1pdm/{segment}/exclude-sites.txt"
@@ -122,6 +123,7 @@ builds:
           filters: --query "(passage_category != 'egg') & (is_reference == True)" --min-date {reference_min_date}
   h3n2_2y:
     lineage: "h3n2"
+    prioritized_seqs_file: "profiles/upload/h3n2/{segment}/prioritized_seqs_file.tsv"
     reference: "config/h3n2/{segment}/reference.fasta"
     annotation: "config/h3n2/{segment}/genemap.gff"
     tree_exclude_sites: "config/h3n2/{segment}/exclude-sites.txt"
@@ -180,6 +182,7 @@ builds:
     subsamples: *representative-subsampling-scheme
   vic_2y:
     lineage: vic
+    prioritized_seqs_file: "profiles/upload/vic/{segment}/prioritized_seqs_file.tsv"
     reference: "config/vic/{segment}/reference.fasta"
     annotation: "config/vic/{segment}/genemap.gff"
     tree_exclude_sites: "config/vic/{segment}/exclude-sites.txt"

diff --git a/profiles/upload/h1n1pdm/ha/prioritized_seqs_file.tsv b/profiles/upload/h1n1pdm/ha/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h1n1pdm/mp/prioritized_seqs_file.tsv b/profiles/upload/h1n1pdm/mp/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h1n1pdm/na/prioritized_seqs_file.tsv b/profiles/upload/h1n1pdm/na/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h1n1pdm/np/prioritized_seqs_file.tsv b/profiles/upload/h1n1pdm/np/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h1n1pdm/ns/prioritized_seqs_file.tsv b/profiles/upload/h1n1pdm/ns/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h1n1pdm/pa/prioritized_seqs_file.tsv b/profiles/upload/h1n1pdm/pa/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h1n1pdm/pb1/prioritized_seqs_file.tsv b/profiles/upload/h1n1pdm/pb1/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h1n1pdm/pb2/prioritized_seqs_file.tsv b/profiles/upload/h1n1pdm/pb2/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h3n2/ha/prioritized_seqs_file.tsv b/profiles/upload/h3n2/ha/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h3n2/mp/prioritized_seqs_file.tsv b/profiles/upload/h3n2/mp/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h3n2/na/prioritized_seqs_file.tsv b/profiles/upload/h3n2/na/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h3n2/np/prioritized_seqs_file.tsv b/profiles/upload/h3n2/np/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h3n2/ns/prioritized_seqs_file.tsv b/profiles/upload/h3n2/ns/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h3n2/pa/prioritized_seqs_file.tsv b/profiles/upload/h3n2/pa/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h3n2/pb1/prioritized_seqs_file.tsv b/profiles/upload/h3n2/pb1/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/h3n2/pb2/prioritized_seqs_file.tsv b/profiles/upload/h3n2/pb2/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/vic/ha/prioritized_seqs_file.tsv b/profiles/upload/vic/ha/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/vic/mp/prioritized_seqs_file.tsv b/profiles/upload/vic/mp/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/vic/na/prioritized_seqs_file.tsv b/profiles/upload/vic/na/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/vic/np/prioritized_seqs_file.tsv b/profiles/upload/vic/np/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/vic/ns/prioritized_seqs_file.tsv b/profiles/upload/vic/ns/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/vic/pa/prioritized_seqs_file.tsv b/profiles/upload/vic/pa/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/vic/pb1/prioritized_seqs_file.tsv b/profiles/upload/vic/pb1/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession
diff --git a/profiles/upload/vic/pb2/prioritized_seqs_file.tsv b/profiles/upload/vic/pb2/prioritized_seqs_file.tsv
@@ -0,0 +1 @@
+strain	accession