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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,126 @@ | ||
| from __future__ import print_function, division | ||
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| import sys | ||
| from collections import defaultdict | ||
| from base_decider import base_Coordinator | ||
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| class FusionCoordinator(base_Coordinator): | ||
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| ''' | ||
| Return a string that is the name that will be used to name the touchfile path | ||
| ''' | ||
| def get_pipeline_name(self): | ||
| return 'Fusion' | ||
|
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| ''' | ||
| Return a dictionary of CWL option to reference file name so this information | ||
| can be added to the parameterized JSON input to the pipeline | ||
| ''' | ||
| def get_cgp_job_reference_files(self): | ||
| cwl_option_to_reference_file_name = defaultdict() | ||
|
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| #Add the correct CWL option and reference file names here | ||
| cwl_option_to_reference_file_name['index'] = "STARFusion-GRCh38gencode23.tar.gz" | ||
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| return cwl_option_to_reference_file_name | ||
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| ''' | ||
| Returns a dictionary of keyword used in the dockstore tool runner parameterized JSON | ||
| and used in Elastic search to find needed samples. The JSON data does not depend | ||
| on samples found in the Elastic search so can be added here | ||
| ''' | ||
| def get_pipeline_job_fixed_metadata(self): | ||
| cgp_pipeline_job_fixed_metadata = defaultdict() | ||
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| cgp_pipeline_job_fixed_metadata["launch_type"] = "tool" | ||
| cgp_pipeline_job_fixed_metadata["analysis_type"] = "fusion_variant_calling" | ||
| cgp_pipeline_job_fixed_metadata["target_tool_prefix"] = 'registry.hub.docker.com/ucsctreehouse/fusion' | ||
| cgp_pipeline_job_fixed_metadata["target_tool_url"] = \ | ||
| "https://dockstore.org/containers/registry.hub.docker.com/ucsctreehouse/fusion/" | ||
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| cgp_pipeline_job_fixed_metadata["input_data_analysis_type"] = "sequence_upload" | ||
| cgp_pipeline_job_fixed_metadata["input_data_experimental_design"] = "RNA-Seq" | ||
| cgp_pipeline_job_fixed_metadata["normal_missing_item"] = "normal_fusion_workflow_0_2_x" | ||
| cgp_pipeline_job_fixed_metadata["normal_present_item"] = "normal_fusion_workflow_0_2_x" | ||
| cgp_pipeline_job_fixed_metadata["tumor_missing_item"] = "tumor_fusion_workflow_0_2_x" | ||
| cgp_pipeline_job_fixed_metadata["tumor_present_item"] = "tumor_fusion_workflow_0_2_x" | ||
| cgp_pipeline_job_fixed_metadata["normal_metadata_flag"] = "normal_fusion_workflow_0_2_x" | ||
| cgp_pipeline_job_fixed_metadata["tumor_metadata_flag"] = "tumor_fusion_workflow_0_2_x" | ||
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| return cgp_pipeline_job_fixed_metadata | ||
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| ''' | ||
| Returns a dictionary of keywords to metadata that is used to setup the touch file path | ||
| and metadata and dockstore JSON file names. These sometimes depend on the sample name | ||
| or other information found through the Elastic search so is separated from the method | ||
| that gets the fixed metadata. This routine adds to the metadata dictionary for the pipeline. | ||
| ''' | ||
| def get_pipeline_job_customized_metadata(self, cgp_pipeline_job_metadata): | ||
| cgp_pipeline_job_metadata['file_prefix'] = cgp_pipeline_job_metadata["submitter_sample_id"] | ||
| cgp_pipeline_job_metadata['metadata_json_file_name'] = cgp_pipeline_job_metadata['file_prefix'] + '_meta_data.json' | ||
| cgp_pipeline_job_metadata["last_touch_file_folder_suffix"] = "" | ||
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| return cgp_pipeline_job_metadata | ||
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| ''' | ||
| Edit the following lines to set up the pipeline tool/workflow CWL options. This method | ||
| returns a dictionary of CWL keywords and values that make up the CWL input parameterized | ||
| JSON for the pipeline. This is the input to the pipeline to be run from Dockstore. | ||
| ''' | ||
| def get_pipeline_parameterized_json(self, cgp_pipeline_job_metadata, analysis): | ||
| cgp_pipeline_job_json = defaultdict() | ||
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| for file in analysis["workflow_outputs"]: | ||
| print("\nfile type:"+file["file_type"]) | ||
| print("\nfile name:"+file["file_path"]) | ||
|
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| #if (file["file_type"] != "bam"): output an error message? | ||
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| file_path = 'redwood' + '://' + self.redwood_host + '/' + analysis['bundle_uuid'] + '/' + \ | ||
| self.fileToUUID(file["file_path"], analysis["bundle_uuid"]) + \ | ||
| "/" + file["file_path"] | ||
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| if 'fastq1' not in cgp_pipeline_job_json.keys(): | ||
| cgp_pipeline_job_json['fastq1'] = defaultdict(dict) | ||
| cgp_pipeline_job_json['fastq1'] = {"class" : "File", "path" : file_path} | ||
| elif 'fastq2' not in cgp_pipeline_job_json.keys(): | ||
| cgp_pipeline_job_json['fastq2'] = defaultdict(dict) | ||
| cgp_pipeline_job_json['fastq2'] = {"class" : "File", "path" : file_path} | ||
| else: | ||
| print("ERROR: Too many input files for Fusion pipeline in analysis output; extra file is:{}!!!".format(file_path), file=sys.stderr) | ||
| return []; | ||
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| if 'parent_uuids' not in cgp_pipeline_job_metadata.keys(): | ||
| cgp_pipeline_job_metadata["parent_uuids"] = [] | ||
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| if cgp_pipeline_job_metadata["sample_uuid"] not in cgp_pipeline_job_metadata["parent_uuids"]: | ||
| cgp_pipeline_job_metadata["parent_uuids"].append(cgp_pipeline_job_metadata["sample_uuid"]) | ||
|
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| cgp_pipeline_job_json["outputdir"] = '.' | ||
| cgp_pipeline_job_json["root-ownership"] = True | ||
| cgp_pipeline_job_json["cpu"] = 32 | ||
|
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| # Specify the output files here, using the options in the CWL file as keys | ||
| file_path = "/tmp/star-fusion-gene-list-filtered.final" | ||
| cgp_pipeline_job_json["output1"] = {"class" : "File", "path" : file_path} | ||
| file_path = "/tmp/star-fusion-gene-list-filtered.final.bedpe" | ||
| cgp_pipeline_job_json["output2"] = {"class" : "File", "path" : file_path} | ||
| file_path = "/tmp/star-fusion-non-filtered.final" | ||
| cgp_pipeline_job_json["output3"] = {"class" : "File", "path" : file_path} | ||
| file_path = "/tmp/star-fusion-non-filtered.final.bedpe" | ||
| cgp_pipeline_job_json["output4"] = {"class" : "File", "path" : file_path} | ||
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| if 'fastq1' not in cgp_pipeline_job_json.keys() or 'fastq2' not in cgp_pipeline_job_json.keys(): | ||
| #we must have paired end reads for the Fusion pipeline so return an empty | ||
| #list to indicate an error if we get here | ||
| print("\nERROR: UNABLE TO GET BOTH FASTQ FILES FOR FUSION PIPELINE; INCOMPLETE JSON IS:{}".format(cgp_pipeline_job_json) , file=sys.stderr) | ||
| return []; | ||
| else: | ||
| return cgp_pipeline_job_json | ||
|
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|
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| if __name__ == '__main__': | ||
| luigi.run() | ||
|
|
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