"metadata":metadata, "metadata_labels":metadata_labels, "picard":args.input_picard, "picard_ext":args.input_picard_extension} # listing all expected input files input_desc+=files.SixteenS.list_file_path_description("",input_files) if not args.exclude_workflow_info: templates += [utilities.get_package_file("workflow_info")] # add the document to the workflow doc_task=workflow.add_document( templates=templates, depends=methoddepends, targets=workflow.name_output_files("16S_report."+args.format), vars=methodvars, table_of_contents=True) # add an archive of the document and figures, removing the log file # the archive will have the same name and location as the output folder workflow.add_archive( depends=[args.output,doc_task], targets=args.output+".zip", remove_log=True) # start the workflow workflow.go()
templates = [ utilities.get_package_file("header"), utilities.get_package_file("stats") ] # add the document to the workflow doc_task = workflow.add_document( templates=templates, depends=maaslin_tasks + stratified_plots_tasks + [taxonomic_profile] + additional_stats_tasks, targets=workflow.name_output_files("stats_report." + args.format), vars={ "title": "Stats Report", "project": args.project_name, "introduction_text": args.introduction_text, "taxonomic_profile": taxonomic_profile, "maaslin_tasks_info": maaslin_tasks_info, "bypass_maaslin": args.bypass_maaslin, "stratified_pathways_plots": stratified_pathways_plots, "permanova_plots": permanova_plots, "beta_diversity_plots": beta_diversity_plots, "covariate_equation": covariate_equation, "format": args.format }, table_of_contents=True) # add an archive of the document and figures, removing the log file # the archive will have the same name and location as the output folder workflow.add_archive(depends=[args.output, doc_task], targets=args.output + ".zip", remove_log=True)
doc_task = workflow.add_document( templates=templates, depends=[wmgx_qc_counts, wmtx_qc_counts, taxonomic_profile, pathabundance], targets=workflow.name_output_files("wmgx_wmtx_report." + args.format), vars={ "title": "Metagenome and Metatranscriptome Report", "project": args.project_name, "introduction_text": args.introduction_text, "dna_read_counts": wmgx_qc_counts, "rna_read_counts": wmtx_qc_counts, "dna_aligned_read_counts": files.ShotGun.path("humann2_read_counts", wmgx_input_folder, none_if_not_found=True), "rna_aligned_read_counts": files.ShotGun.path("humann2_read_counts", wmtx_input_folder, none_if_not_found=True), "dna_feature_counts": files.ShotGun.path("feature_counts", wmgx_input_folder, none_if_not_found=True), "rna_feature_counts": files.ShotGun.path("feature_counts", wmtx_input_folder, none_if_not_found=True), "taxonomic_profile": taxonomic_profile, "dna_pathabundance": pathabundance, "genefamilies_norm_ratio": files.ShotGun.path("genefamilies_norm_ratio", args.input, none_if_not_found=True), "ecs_norm_ratio": files.ShotGun.path("ecs_norm_ratio", args.input, none_if_not_found=True), "paths_norm_ratio": files.ShotGun.path("paths_norm_ratio", args.input, none_if_not_found=True), "format": args.format, "log": log_file }, table_of_contents=True)
os.path.join(args.output, 'data', os.path.basename(files + "_backup")) for files in multiple_input_files ] workflow.add_task_group( "cp [depends[0]] [targets[0]]", #Command depends=[multiple_input_files], #Tracking executable dependencies targets=output_files) #Output target directory # private python function definition def remove_end_tabs_function(task): with open(task.targets[0].name, 'w') as file_handle_out: for line in open(task.depends[0].name): file_handle_out.write(line.rstrip() + "\n") # Task4 add_task - AnADAMA2 example to usage of python task function workflow.add_task( remove_end_tabs_function, #Calling the python function depends=args.input, #Tracking executable dependencies targets=args.output + "/data/data.tsv.notabs", #Target output name="remove_end_tabs") #Task5 Add the document to the workflow pdf_report = os.path.join(os.getcwd(), args.output, "pdfReport.pdf") workflow.add_document(templates="doc/template.py", targets=pdf_report, vars={"introduction_text": "Demo Title"}) # Run the workflow workflow.go()
templates += [utilities.get_package_file("workflow_info")] log_file = files.Workflow.path("log", args.input, error_if_not_found=True) # add the document to the workflow doc_task = workflow.add_document( templates=templates, depends=[ qc_counts, taxonomic_profile, pathabundance, read_counts, feature_counts ], targets=workflow.name_output_files("wmgx_report." + args.format), vars={ "title": "Metagenome Report", "project": args.project_name, "introduction_text": args.introduction_text, "dna_read_counts": qc_counts, "taxonomic_profile": taxonomic_profile, "dna_pathabundance": pathabundance, "dna_ecabundance": ecsabundance, "read_counts": read_counts, "feature_counts": feature_counts, "format": args.format, "log": log_file, "metadata": metadata, "metadata_labels": metadata_labels }, table_of_contents=True) # add an archive of the document and figures, removing the log file # the archive will have the same name and location as the output folder workflow.add_archive(depends=[args.output, doc_task],