use sample query for ci speed

sanjaynagi · Aug 18, 2023 · ba0b53a · ba0b53a
1 parent 5841b6e
commit ba0b53a
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Showing 5 changed files with 11 additions and 6 deletions.
diff --git a/notebooks/AgamPrimer-long.ipynb b/notebooks/AgamPrimer-long.ipynb
@@ -101,7 +101,8 @@
         "#@markdown primer_target should be a region string ('2L:28545767') for gDNA primers and probes, and an AGAP transcript identifier for cDNA primers.\n",
         "\n",
         "primer_target = 'AGAP006228-RA'      #@param {type:\"string\"} \n",
-        "sample_sets = 'AG1000G-GH'           #@param {type:\"string\"}"
+        "sample_sets = 'AG1000G-GH'           #@param {type:\"string\"}\n",
+        "sample_query = None #'taxon == \"coluzzii\"' "
       ]
     },
     {
@@ -429,7 +430,7 @@
       "outputs": [],
       "source": [
         "#sample_sets = None  #'AG1000G-GH'          # sample_set = '3.0' .you can also supply lists with multiple sample sets e.g ['AG1000G-GH', 'AG1000G-CI', 'AG1000G-BF-A']\n",
-        "sample_query = None  #\"taxon == 'coluzzii'\"                # here we can subset to specific values in the metadata e.g :     \"taxon == 'gambiae'\" , or \"taxon == 'arabiensis'\"          "
+        "#sample_query = None  #\"taxon == 'coluzzii'\"                # here we can subset to specific values in the metadata e.g :     \"taxon == 'gambiae'\" , or \"taxon == 'arabiensis'\"          "
       ]
     },
     {

diff --git a/tests/cDNA_Params.json b/tests/cDNA_Params.json
@@ -6,5 +6,6 @@
     "max_amplicon_size": 120,
     "n_primer_pairs":6,
     "primer_target": "AGAP006228-RA",
-    "sample_sets": "AG1000G-GH"
+    "sample_sets": "AG1000G-GH",
+    "sample_query":"taxon == 'coluzzii"
 }
diff --git a/tests/cDNA_Params_2.json b/tests/cDNA_Params_2.json
@@ -7,5 +7,6 @@
     "n_primer_pairs":6,
     "primer_target": "AGAP028081-RA",
     "cDNA_exon_junction" : false,
-    "sample_sets": "AG1000G-GH"
+    "sample_sets": "AG1000G-GH",
+    "sample_query":"taxon == 'coluzzii"
 }
diff --git a/tests/gDNA_probe_Params.json b/tests/gDNA_probe_Params.json
@@ -6,5 +6,6 @@
     "max_amplicon_size": 100,
     "n_primer_pairs":4,
     "primer_target": "2L:2422652",
-    "sample_sets": "AG1000G-GH"
+    "sample_sets": "AG1000G-GH",
+    "sample_query":"taxon == 'coluzzii"
 }
diff --git a/tests/probe_Params.json b/tests/probe_Params.json
@@ -6,5 +6,6 @@
     "max_amplicon_size": 240,
     "n_primer_pairs":6,
     "primer_target": "X:9500000",
-    "sample_sets": "AG1000G-GH"
+    "sample_sets": "AG1000G-GH",
+    "sample_query":"taxon == 'coluzzii"
 }