"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],
