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djgomezsantos · Aug 7, 2024 · d855591 · d855591
1 parent b772173
commit d855591
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Showing 10 changed files with 16 additions and 13 deletions.
diff --git a/bin/convert_to_ometiff.py b/bin/convert_to_ometiff.py
@@ -95,7 +95,12 @@ def create_original_channel_names_df(channelList: List[str]) -> pd.DataFrame:
     ].str.extract(cyc_ch_pattern)
     og_ch_names_df["Cycle"] = pd.to_numeric(og_ch_names_df["Cycle"])
     og_ch_names_df["Channel"] = pd.to_numeric(og_ch_names_df["Channel"])
-    og_ch_names_df["channel_id"] = "cycle" + og_ch_names_df["Cycle"].astype(str) + "_ch" + og_ch_names_df["Channel"].astype(str)
+    og_ch_names_df["channel_id"] = (
+        "cycle"
+        + og_ch_names_df["Cycle"].astype(str)
+        + "_ch"
+        + og_ch_names_df["Channel"].astype(str)
+    )
 
     return og_ch_names_df
 
@@ -379,9 +384,7 @@ def check_dir_is_empty(dir_path: Path):
     antb_info = get_ch_info_from_antibodies_meta(df)
     extractChannelNames = collect_expressions_extract_channels(extractFileList[0])
     original_ch_names_df = create_original_channel_names_df(extractChannelNames)
-    updated_channel_names = replace_provider_ch_names_with_antb(
-        original_ch_names_df, antb_info
-    )
+    updated_channel_names = replace_provider_ch_names_with_antb(original_ch_names_df, antb_info)
 
     # Create segmentation mask OME-TIFFs
     if segmentationFileList:

diff --git a/steps/illumination_first_stitching/best_focus.cwl b/steps/illumination_first_stitching/best_focus.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerPull: hubmap/codex-scripts
+    dockerPull: hubmap/codex-scripts:latest
     dockerOutputDirectory: "/output"
 
 baseCommand: ["python", "/opt/best_focus/run_best_focus_selection.py"]

diff --git a/steps/illumination_first_stitching/collect_dataset_info.cwl b/steps/illumination_first_stitching/collect_dataset_info.cwl
@@ -4,7 +4,7 @@ label: Collect dataset info for Cytokit
 
 requirements:
   DockerRequirement:
-    dockerPull: hubmap/codex-scripts
+    dockerPull: hubmap/codex-scripts:latest
 
 baseCommand: ["python", "/opt/dataset_info/run_collection.py"]
 

diff --git a/steps/illumination_first_stitching/create_yaml_config.cwl b/steps/illumination_first_stitching/create_yaml_config.cwl
@@ -4,7 +4,7 @@ label: Create Cytokit experiment config
 
 requirements:
   DockerRequirement:
-    dockerPull: hubmap/codex-scripts
+    dockerPull: hubmap/codex-scripts:latest
 
 baseCommand: ["python", "/opt/create_cytokit_config.py"]
 

diff --git a/steps/illumination_first_stitching/first_stitching.cwl b/steps/illumination_first_stitching/first_stitching.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerPull: hubmap/codex-scripts
+    dockerPull: hubmap/codex-scripts:latest
     dockerOutputDirectory: "/output"
 
 baseCommand: ["python", "/opt/codex_stitching/run_stitching.py"]

diff --git a/steps/illumination_first_stitching/illumination_correction.cwl b/steps/illumination_first_stitching/illumination_correction.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerPull: hubmap/codex-scripts
+    dockerPull: hubmap/codex-scripts:latest
     dockerOutputDirectory: "/output"
 
 baseCommand: ["python", "/opt/illumination_correction/run_illumination_correction.py"]

diff --git a/steps/illumination_first_stitching/slicing.cwl b/steps/illumination_first_stitching/slicing.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerPull: hubmap/codex-scripts
+    dockerPull: hubmap/codex-scripts:latest
     dockerOutputDirectory: "/output"
 
 baseCommand: ["python", "/opt/slicing/run_slicing.py"]

diff --git a/steps/ometiff_second_stitching/background_subtraction.cwl b/steps/ometiff_second_stitching/background_subtraction.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerPull: hubmap/codex-scripts
+    dockerPull: hubmap/codex-scripts:latest
     dockerOutputDirectory: "/output"
 
 baseCommand: ["python", "/opt/background_subtraction/run_background_subtraction.py"]

diff --git a/steps/ometiff_second_stitching/ome_tiff_creation.cwl b/steps/ometiff_second_stitching/ome_tiff_creation.cwl
@@ -4,7 +4,7 @@ label: Create OME-TIFF versions of Cytokit segmentation and extract results
 
 requirements:
   DockerRequirement:
-    dockerPull: hubmap/codex-scripts
+    dockerPull: hubmap/codex-scripts:latest
 
 baseCommand: ["python", "/opt/convert_to_ometiff.py"]
 

diff --git a/steps/ometiff_second_stitching/second_stitching.cwl b/steps/ometiff_second_stitching/second_stitching.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerPull: hubmap/codex-scripts
+    dockerPull: hubmap/codex-scripts:latest
     dockerOutputDirectory: /output
 
 baseCommand: ["python", "/opt/codex_stitching/secondary_stitcher/secondary_stitcher_runner.py"]