diff --git a/workflows/spaceranger/spaceranger_workflow.wdl b/workflows/spaceranger/spaceranger_workflow.wdl index 388acd74..3916bb06 100644 --- a/workflows/spaceranger/spaceranger_workflow.wdl +++ b/workflows/spaceranger/spaceranger_workflow.wdl @@ -4,7 +4,7 @@ import "spaceranger_count.wdl" as src workflow spaceranger_workflow { input { - # Columns: Sample, Reference, Flowcell, [ProbeSet, Image, DarkImage, ColorizedImage, CytaImage, Slide, Area, SlideFile, LoupeAlignment, TargetPanel]) + # Columns: Sample, Reference, Flowcell, [ProbeSet, Image, DarkImage, ColorizedImage, CytaImage, Slide, Area, SlideFile, LoupeAlignment]) File input_csv_file # Output directory, gs URL String output_directory @@ -103,7 +103,6 @@ workflow spaceranger_workflow { slidefile = sample_row[10], reorient_images = reorient_images, loupe_alignment = sample_row[11], - target_panel = sample_row[12], no_bam = no_bam, secondary = secondary, r1_length = r1_length, @@ -178,7 +177,7 @@ task generate_count_config { print('Examples of common characters that are not allowed are the space character and the following: ?()[]/\=+<>:;"\',*^| &', file = sys.stderr) sys.exit(1) - for c in ['Image', 'ColorizedImage', 'CytaImage', 'SlideFile', 'LoupeAlignment', 'TargetPanel']: + for c in ['Image', 'ColorizedImage', 'CytaImage', 'SlideFile', 'LoupeAlignment']: if c not in df.columns: df[c] = '~{null_file}' else: @@ -204,7 +203,7 @@ task generate_count_config { df_local = df.loc[df['Sample'] == sample_id] dirs = df_local['Flowcell'].values out_str = df_local['Sample'].iat[0] + '\t' + ','.join(dirs) + '\t' + df_local['Reference'].iat[0] - for c in ['ProbeSet', 'Image', 'DarkImage', 'ColorizedImage', 'CytaImage', 'Slide', 'Area', 'SlideFile', 'LoupeAlignment', 'TargetPanel']: + for c in ['ProbeSet', 'Image', 'DarkImage', 'ColorizedImage', 'CytaImage', 'Slide', 'Area', 'SlideFile', 'LoupeAlignment']: out_str += '\t' + df_local[c].iat[0] print(out_str) CODE