Recipes need tomo relion options, and pixel size name change

DiamondLightSource · Aug 21, 2024 · 6fa62cb · 6fa62cb
1 parent d90fad2
commit 6fa62cb
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Showing 4 changed files with 10 additions and 28 deletions.
diff --git a/recipes/em-spa-extract.json b/recipes/em-spa-extract.json
@@ -17,7 +17,7 @@
       "micrographs_file": "{micrographs_file}",
       "output_file": "{output_file}",
       "particle_diameter": "{particle_diameter}",
-      "pixel_size": "{pix_size}",
+      "pixel_size": "{pixel_size}",
       "relion_options": {},
       "voltage": "{kv}"
     },
@@ -44,10 +44,5 @@
     "queue": "{feedback_queue}",
     "service": "Murfey"
   },
-  "start": [
-    [
-      1,
-      []
-    ]
-  ]
+  "start": [[1, []]]
 }
diff --git a/recipes/em-spa-preprocess.json b/recipes/em-spa-preprocess.json
@@ -53,7 +53,7 @@
       "movie_id": "$ispyb_movie_id",
       "mrc_out": "{mrc_out}",
       "picker_uuid": "{picker_uuid}",
-      "pixel_size": "{pix_size}",
+      "pixel_size": "{pixel_size}",
       "relion_options": {},
       "threads": 4,
       "voltage": "{kv}"
@@ -115,10 +115,5 @@
     "queue": "ispyb_connector",
     "service": "EMISPyB"
   },
-  "start": [
-    [
-      1,
-      []
-    ]
-  ]
+  "start": [[1, []]]
 }
diff --git a/recipes/em-tomo-align.json b/recipes/em-tomo-align.json
@@ -14,7 +14,8 @@
       "input_file_list": "{input_file_list}",
       "manual_tilt_offset": "{manual_tilt_offset}",
       "path_pattern": "{path_pattern}",
-      "pixel_size": "{pix_size}",
+      "pixel_size": "{pixel_size}",
+      "relion_options": {},
       "stack_file": "{stack_file}"
     },
     "queue": "tomo_align",
@@ -71,10 +72,5 @@
     "queue": "segmentation",
     "service": "MembrainSeg"
   },
-  "start": [
-    [
-      1,
-      []
-    ]
-  ]
+  "start": [[1, []]]
 }
diff --git a/recipes/em-tomo-preprocess.json b/recipes/em-tomo-preprocess.json
@@ -32,7 +32,8 @@
       "movie_id": "$ispyb_movie_id",
       "mrc_out": "{mrc_out}",
       "picker_uuid": "-1",
-      "pixel_size": "{pix_size}",
+      "pixel_size": "{pixel_size}",
+      "relion_options": {},
       "voltage": "{kv}"
     },
     "queue": "motioncorr",
@@ -77,10 +78,5 @@
     "queue": "ispyb_connector",
     "service": "EMISPyB"
   },
-  "start": [
-    [
-      1,
-      []
-    ]
-  ]
+  "start": [[1, []]]
 }