From da20932ffc9457aa74e107d8759934d178e413de Mon Sep 17 00:00:00 2001 From: Carmen Diaz Verdugo Date: Wed, 11 Jan 2023 16:22:33 -0500 Subject: [PATCH 1/2] Update cpd_analysis_pipeline.wdl cpd_analysis_pipeline should get as an input load_data_with_illum.csv and not load_data.csv. It is more clear for the person running the workflow --- pipelines/cellpainting/cpd_analysis_pipeline.wdl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pipelines/cellpainting/cpd_analysis_pipeline.wdl b/pipelines/cellpainting/cpd_analysis_pipeline.wdl index 5e661ae..2bac2be 100644 --- a/pipelines/cellpainting/cpd_analysis_pipeline.wdl +++ b/pipelines/cellpainting/cpd_analysis_pipeline.wdl @@ -14,7 +14,7 @@ workflow cpd_analysis_pipeline { # Specify input file information String images_directory_gsurl - File load_data_csv + File load_data_with_illum_csv String illum_directory_gsurl = "${images_directory}/illum" # Cellprofiler pipeline specification @@ -46,7 +46,7 @@ workflow cpd_analysis_pipeline { # Create an index to scatter call util.scatter_index as idx { input: - load_data_csv= load_data_csv, + load_data_csv= load_data_with_illum_csv, splitby_metadata = splitby_metadata, } @@ -56,7 +56,7 @@ workflow cpd_analysis_pipeline { input: image_directory = images_directory, illum_directory = illum_directory, - load_data_csv = load_data_csv, + load_data_csv = load_data_with_illum_csv, splitby_metadata = splitby_metadata, index = index, } From 41212936d20c971823245b678eb835c41f27e4b7 Mon Sep 17 00:00:00 2001 From: Carmen Diaz Verdugo Date: Wed, 11 Jan 2023 16:30:17 -0500 Subject: [PATCH 2/2] Update cellpainting_workflow.wdl --- tests/cellpainting_workflow.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/cellpainting_workflow.wdl b/tests/cellpainting_workflow.wdl index a3e21a8..1e62cdd 100644 --- a/tests/cellpainting_workflow.wdl +++ b/tests/cellpainting_workflow.wdl @@ -92,7 +92,7 @@ workflow cellpainting_workflow { input: images_directory_gsurl = cp_illumination.images_output_directory, # illum_directory_gsurl = cp_illumination.illum_output_directory, - load_data_csv = cpd_max_projection.load_data_with_illum_csv, + load_data_with_illum_csv = cpd_max_projection.load_data_with_illum_csv, cppipe_file = analysis_cppipe_file, output_directory_gsurl = analysis_output_directory_gsurl, } @@ -115,4 +115,4 @@ workflow cellpainting_workflow { output_directory_url = mining_directory_gsurl, } -} \ No newline at end of file +}