add directory input handling

Author: bmeluch

Makefile

@@ -106,13 +106,21 @@ cascade-run:
 cli-run-di :
 	enviroMS run_di configuration/di_enviroms.toml --jobs 1 --replicas 1 --tasks 1
 
-wdl-run-di :
+wdl-run-di-thermo :
 
-	miniwdl run wdl/di_fticr_ms.wdl -i wdl/di_fticr_wdl_input.json --verbose --no-cache --copy-input-files
+	miniwdl run wdl/di_fticr_ms_thermo.wdl -i wdl/di_fticr_wdl_input.json --verbose --no-cache --copy-input-files
 
-wdl-run-di-local :
+wdl-run-di-thermo-local :
 	@make docker-build-local
-	miniwdl run wdl/di_fticr_ms.wdl -i wdl/di_fticr_wdl_input_local_docker.json --verbose --no-cache --copy-input-files
+	miniwdl run wdl/di_fticr_ms_thermo.wdl -i wdl/di_fticr_wdl_input_local_docker.json --verbose --no-cache --copy-input-files
+
+wdl-run-di-bruker :
+ 	 
+	miniwdl run wdl/di_fticr_ms_bruker.wdl -i wdl/di_fticr_wdl_input.json --verbose --no-cache --copy-input-files
+
+wdl-run-di-bruker-local :
+	@make docker-build-local
+	miniwdl run wdl/di_fticr_ms_bruker.wdl -i wdl/di_fticr_wdl_input_local_docker.json --verbose --no-cache --copy-input-files
 
 wdl-run-lc :
 

README.md

@@ -165,8 +165,11 @@ pip3 install miniwdl
 ```
 
 For Direct Infusion Workflow:
+
+_Note that for the direct infusion workflow, the WDL file used depends on the instrument/output file type. Use "Bruker" WDL for .d files and "Thermo" WDL for ".raw" files._
+
 ```bash
-miniwdl run wdl/di_fticr_ms.wdl -i wdl/di_fticr_wdl_input.json --verbose --no-cache --copy-input-files
+miniwdl run wdl/di_fticr_ms_bruker.wdl -i wdl/di_fticr_wdl_input.json --verbose --no-cache --copy-input-files
 ```
 For Liquid Chromatography Workflow:
 ```bash

wdl/di_fticr_ms_bruker.wdl

@@ -0,0 +1,84 @@
+version 1.2
+
+workflow fticrmsNOM {
+    input {
+        String? docker_image  # Optional input for Docker image
+    }
+
+    call runDirectInfusion {
+        input:
+            docker_image = docker_image
+    }
+
+    output {
+        String out = runDirectInfusion.out
+        Array[File] output_files = runDirectInfusion.output_files
+        Array[File] van_krevelen_plots = runDirectInfusion.van_krevelen_plots
+        Array[File] dbe_vs_c_plots = runDirectInfusion.dbe_vs_c_plots
+        Array[File] ms_class_plots = runDirectInfusion.ms_class_plots
+        Array[File] mz_error_class_plots = runDirectInfusion.mz_error_class_plots
+        Array[File] qc_plots = runDirectInfusion.qc_plots
+    }
+}
+
+task runDirectInfusion {
+    input {
+        Array[Directory] file_paths
+        String output_directory
+        String output_type
+        File corems_toml_path
+        String polarity
+        Int raw_file_start_scan
+        Int raw_file_final_scan
+        Boolean is_centroid
+        File calibration_ref_file_path
+        Boolean calibrate
+        Boolean batch_calibrate
+        Boolean plot_mz_error
+        Boolean plot_ms_assigned_unassigned
+        Boolean plot_c_dbe
+        Boolean plot_van_krevelen
+        Boolean plot_ms_classes
+        Boolean plot_mz_error_classes
+        Boolean plot_qc
+        Int jobs_count = 1
+        String? docker_image
+    }
+
+    command {
+        enviroMS run_di_wdl \
+            ${sep=',' file_paths} \
+            ${output_directory} \
+            ${output_type} \
+            ${corems_toml_path} \
+            ${polarity} \
+            ${raw_file_start_scan} \
+            ${raw_file_final_scan} \
+            ${is_centroid} \
+            ${calibration_ref_file_path} \
+            -c ${calibrate} \
+            -bc ${batch_calibrate} \
+            -e ${plot_mz_error} \
+            -a ${plot_ms_assigned_unassigned} \
+            -cb ${plot_c_dbe} \
+            -vk ${plot_van_krevelen} \
+            -mc ${plot_ms_classes} \
+            -ec ${plot_mz_error_classes} \
+            -qc ${plot_qc} \
+            --jobs ${jobs_count}
+    }
+
+    output {
+        String out = read_string(stdout())
+        Array[File] output_files = glob('${output_directory}/**/*.*')
+        Array[File] van_krevelen_plots = glob('${output_directory}/**/van_krevelen/*.*')
+        Array[File] dbe_vs_c_plots = glob('${output_directory}/**/dbe_vs_c/*.*')
+        Array[File] ms_class_plots = glob('${output_directory}/**/ms_class/*.*')
+        Array[File] mz_error_class_plots = glob('${output_directory}/**/mz_error_class/*.*')
+        Array[File] qc_plots = glob('${output_directory}/**/qc_plots/*.*')
+    }
+
+    runtime {
+        docker: "~{if defined(docker_image) then docker_image else 'microbiomedata/enviroms:5.1.0'}"
+    }
+}

wdl/di_fticr_ms.wdl wdl/di_fticr_ms_thermo.wdlwdl/di_fticr_ms.wdl renamed to wdl/di_fticr_ms_thermo.wdl

@@ -1,4 +1,4 @@
-version 1.0
+version 1.2
 
 workflow fticrmsNOM {
     input {

wdl/lc_fticr_ms.wdl

@@ -1,4 +1,4 @@
-version 1.0
+version 1.2
 
 workflow lc_ft_icr_ms {
     input {