Merge pull request #36 from mskcc/feature/intermediate_metrics

Added output folder for intermediate metrics

modules/project/generate-qc.cwl

@@ -97,7 +97,7 @@ outputs:
 
   consolidated_results:
     type: Directory
-    outputSource: consolidate_results/directory
+    outputSource: consolidate_metrics/directory
   qc_pdf:
     type: File
     outputSource: generate_qc/qc_pdf
@@ -185,9 +185,6 @@ steps:
   put-conpair-files-into-directory:
     run: ../../tools/conpair/0.3.3/consolidate-conpair-files.cwl
     in:
-      concordance_files: run-concordance/outfiles
-      concordance_files_nohomo: run-concordance-non-homozygous/outfiles
-      contamination_files: run-contamination/outfiles
       files:
         source: [ run-concordance/outfiles, run-concordance-non-homozygous/outfiles, run-contamination/outfiles ]
         linkMerge: merge_flattened
@@ -225,19 +222,45 @@ steps:
       data_dir:  qc_merge_and_hotspots/qc_merged_directory
       file_prefix: project_prefix
     out: [ output, images_directory, project_summary, sample_summary ]
+  consolidate_intermediate_files:
+    run: ../../tools/consolidate-files/consolidate-files-list.cwl
+    in:
+      hs_metrics: hs_metrics
+      md_metrics: md_metrics
+      per_target_coverage: per_target_coverage
+      insert_metrics: insert_metrics
+      doc_basecounts: doc_basecounts
+      qual_metrics: qual_metrics
+      file_lists:
+        valueFrom: ${ var intermediate_metrics = []; intermediate_metrics=intermediate_metrics.concat(inputs.hs_metrics, inputs.md_metrics, inputs.per_target_coverage, inputs.insert_metrics, inputs.doc_basecounts, inputs.qual_metrics); return intermediate_metrics; }
+      output_directory_name:
+        valueFrom: ${ return "intermediate_metrics"; }
+    out: [ directory ]
   consolidate_results:
     run: ../../tools/consolidate-files/consolidate-files-mixed.cwl
     in:
       output_directory_name:
-        valueFrom: ${ return "consolidated_metrics_data"; }
+        valueFrom: ${ return "consolidated_metrics"; }
       input_directories: directories
       conpair_directory: put-conpair-files-into-directory/directory
       qc_merged_and_hotspots_directory: qc_merge_and_hotspots/qc_merged_directory
       generate_images_directory: generate_images/output
       files: files
       directories:
-        valueFrom: ${ var metrics_data = [inputs.qc_merged_and_hotspots_directory, inputs.generate_images_directory, inputs.conpair_directory ]; return metrics_data.concat(inputs.input_directories); }
+        valueFrom: ${ var metrics_data = [inputs.qc_merged_and_hotspots_directory, inputs.generate_images_directory, inputs.conpair_directory]; return metrics_data.concat(inputs.input_directories); }
     out: [ directory ]
+  consolidate_metrics:
+    run: ../../tools/consolidate-files/consolidate-files-mixed.cwl
+    in:
+      consolidated_metrics: consolidate_intermediate_files/directory
+      consolidated_results: consolidate_results/directory
+      output_directory_name:
+        valueFrom: ${ return "qc_metrics"; }
+      directories:
+        valueFrom: ${ return [inputs.consolidated_metrics, inputs.consolidated_results]}
+      flatten_directories:
+        valueFrom: ${ return false; }
+    out: [directory]
   generate_qc:
     run: ../../tools/roslin-qc/genlatex.cwl
     in:

tools/consolidate-files/consolidate-files-list.cwl

@@ -0,0 +1,60 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: ExpressionTool
+id: consolidate-files-list
+
+requirements:
+  - class: InlineJavascriptRequirement
+
+inputs:
+
+  output_directory_name: string
+
+  file_lists:
+    type:
+      type: array
+      items:
+        type: array
+        items:
+          - File
+          - string
+          - 'null'
+
+
+outputs:
+
+  directory:
+    type: Directory
+
+# This tool returns a Directory object,
+# which holds all output files from the list
+# of supplied input file_lists
+expression: |
+  ${
+    var output_files_list = [];
+    function addFile(input_file_list) {
+      var output_files = [];
+      var input_files = input_file_list.filter(single_file => String(single_file).toUpperCase() != 'NONE');
+      for (var i = 0; i < input_file_list.length; i++) {
+        if(input_files[i]){
+          output_files.push(input_file_list[i]);
+        }
+      }
+      return output_files;
+    }
+    for (var i = 0; i < inputs.file_lists.length; i++) {
+      if(inputs.file_lists[i]){
+        output_files_list = output_files_list.concat(addFile(inputs.file_lists[i]));
+      }
+
+    }
+
+    return {
+      'directory': {
+        'class': 'Directory',
+        'basename': inputs.output_directory_name,
+        'listing': output_files_list
+      }
+    };
+  }