diff --git a/bin/convert_to_ometiff.py b/bin/convert_to_ometiff.py index 5e96b4d..3660fe6 100755 --- 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 index 1185cac..075a841 100644 --- 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 index b84aba0..12f1291 100644 --- 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 index 3acec38..806860c 100644 --- 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 index 3e52320..11513e6 100644 --- 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 index d1dea6c..89c01ce 100644 --- 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 index 8e1126f..068a7b5 100644 --- 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 index aeab1e9..a4d0deb 100644 --- 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 index c11f104..6c8cf3f 100644 --- 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 index c431194..660359c 100644 --- 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"]