improve: params in workflows

subugoe · Jul 26, 2024 · 9fd048e · 9fd048e
1 parent 8608036
commit 9fd048e
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Showing 4 changed files with 14 additions and 14 deletions.
diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow.nf
@@ -111,7 +111,7 @@ process ocrd_skimage_binarize {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-skimage-binarize -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
+    ${params.singularity_wrapper} ocrd-skimage-binarize -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P method "li"
     """
 }
 
@@ -132,7 +132,7 @@ process ocrd_skimage_denoise {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-skimage-denoise -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+    ${params.singularity_wrapper} ocrd-skimage-denoise -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P level-of-operation "page"
     """
 }
 
@@ -153,7 +153,7 @@ process ocrd_tesserocr_deskew {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-tesserocr-deskew -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
+    ${params.singularity_wrapper} ocrd-tesserocr-deskew -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P operation_level "page"
     """
 }
 
@@ -174,7 +174,7 @@ process ocrd_cis_ocropy_segment {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-segment -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+    ${params.singularity_wrapper} ocrd-cis-ocropy-segment -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P level-of-operation "page"
     """
 }
 
@@ -216,7 +216,7 @@ process ocrd_calamari_recognize {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-calamari-recognize -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
+    ${params.singularity_wrapper} ocrd-calamari-recognize -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P checkpoint_dir "qurator-gt4histocr-1.0"
     """
 }
 
@@ -237,7 +237,7 @@ process ocrd_fileformat_transform {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-fileformat-transform -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"from-to": "page alto"}'
+    ${params.singularity_wrapper} ocrd-fileformat-transform -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P from-to "page alto"
     """    
 }
 

diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow_with_MS.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/default_workflow_with_MS.nf
@@ -103,7 +103,7 @@ process ocrd_skimage_binarize {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-skimage-binarize -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"method": "li"}'
+    ${params.singularity_wrapper} ocrd-skimage-binarize -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P method "li"
     """
 }
 
@@ -122,7 +122,7 @@ process ocrd_skimage_denoise {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-skimage-denoise -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+    ${params.singularity_wrapper} ocrd-skimage-denoise -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P level-of-operation "page"
     """
 }
 
@@ -141,7 +141,7 @@ process ocrd_tesserocr_deskew {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-tesserocr-deskew -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"operation_level": "page"}'
+    ${params.singularity_wrapper} ocrd-tesserocr-deskew -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P operation_level "page"
     """
 }
 
@@ -160,7 +160,7 @@ process ocrd_cis_ocropy_segment {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-cis-ocropy-segment -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"level-of-operation": "page"}'
+    ${params.singularity_wrapper} ocrd-cis-ocropy-segment -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P level-of-operation "page"
     """
 }
 
@@ -198,7 +198,7 @@ process ocrd_calamari_recognize {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-calamari-recognize -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"checkpoint_dir": "qurator-gt4histocr-1.0"}'
+    ${params.singularity_wrapper} ocrd-calamari-recognize -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P checkpoint_dir "qurator-gt4histocr-1.0"
     """
 }
 
@@ -217,7 +217,7 @@ process ocrd_fileformat_transform {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-fileformat-transform -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"from-to": "page alto"}'
+    ${params.singularity_wrapper} ocrd-fileformat-transform -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P from-to "page alto"
     """
 }
 

diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow.nf
@@ -279,7 +279,7 @@ process ocrd_fileformat_transform_10 {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-fileformat-transform -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"from-to": "page alto"}'
+    ${params.singularity_wrapper} ocrd-fileformat-transform -w ${params.workspace_dir} -m ${mets_file_chunk} --page-id ${page_range} -I ${input_group} -O ${output_group} -P from-to "page alto"
     """    
 }
 

diff --git a/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow_with_MS.nf b/src/utils/operandi_utils/hpc/nextflow_workflows/odem_workflow_with_MS.nf
@@ -255,7 +255,7 @@ process ocrd_fileformat_transform_10 {
 
     script:
     """
-    ${params.singularity_wrapper} ocrd-fileformat-transform -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -p '{"from-to": "page alto"}'
+    ${params.singularity_wrapper} ocrd-fileformat-transform -U ${params.mets_socket} -w ${params.workspace_dir} -m ${params.mets} --page-id ${page_range} -I ${input_group} -O ${output_group} -P from-to "page alto"
     """
 }