auto_process_ngs.cli.auto_process
Automated data processing & QC pipeline for Illumina sequence data
Implements a program for automating stages of a standard protocol for processing and QC’ing Illumina sequencing data.
The stages are:
setup make_fastqs setup_analysis_dirs run_qc publish_qc archive report
The ‘setup’ stage creates an analysis directory and acquires the basic data about the sequencing run from a source directory. Subsequent stages should be run in sequence to create fastq files, set up analysis directories for each project, and run QC scripts for each sample in each project.
The following commands enable the querying and setting of configuration settings and project metadata:
info config params metadata
Additional commands are available:
update clone samplesheet analyse_barcodes merge_fastq_dirs update_fastq_stats import_project readme
but these are not part of the standard workflow - they are used for special cases and testing.
- auto_process_ngs.cli.auto_process.add_analyse_barcodes_command(cmdparser)
Create a parser for the ‘analyse_barcodes’ command
- auto_process_ngs.cli.auto_process.add_archive_command(cmdparser)
Create a parser for the ‘archive’ command
- auto_process_ngs.cli.auto_process.add_clone_command(cmdparser)
Create a parser for the ‘clone’ command
- auto_process_ngs.cli.auto_process.add_config_command(cmdparser)
Create a parser for the ‘config’ command
- auto_process_ngs.cli.auto_process.add_import_project_command(cmdparser)
Create a parser for the ‘import_project’ command
- auto_process_ngs.cli.auto_process.add_info_command(cmdparser)
Create a parser for the ‘info’ command
- auto_process_ngs.cli.auto_process.add_make_fastqs_command(cmdparser)
Create a parser for the ‘make_fastqs’ command
- auto_process_ngs.cli.auto_process.add_merge_fastq_dirs_command(cmdparser)
Create a parser for the ‘merge_fastq_dirs’ command
- auto_process_ngs.cli.auto_process.add_metadata_command(cmdparser)
Create a parser for the ‘metadata’ command
- auto_process_ngs.cli.auto_process.add_params_command(cmdparser)
Create a parser for the ‘params’ command
- auto_process_ngs.cli.auto_process.add_publish_qc_command(cmdparser)
Create a parser for the ‘publish_qc’ command
- auto_process_ngs.cli.auto_process.add_readme_command(cmdparser)
Create a parser for the ‘readme’ command
- auto_process_ngs.cli.auto_process.add_report_command(cmdparser)
Create a parser for the ‘report’ command
- auto_process_ngs.cli.auto_process.add_run_qc_command(cmdparser)
Create a parser for the ‘run_qc’ command
- auto_process_ngs.cli.auto_process.add_samplesheet_command(cmdparser)
Create a parser for the ‘samplesheet’ command
- auto_process_ngs.cli.auto_process.add_setup_analysis_dirs_command(cmdparser)
Create a parser for the ‘setup_analysis_dirs’ command
- auto_process_ngs.cli.auto_process.add_setup_command(cmdparser)
Create a parser for the ‘setup’ command
- auto_process_ngs.cli.auto_process.add_update_command(cmdparser)
Create a parser for the ‘update’ command
- auto_process_ngs.cli.auto_process.add_update_fastq_stats_command(cmdparser)
Create a parser for the ‘update_fastq_stats’ command
- auto_process_ngs.cli.auto_process.analyse_barcodes(args)
Implement functionality for ‘analyse_barcodes’ command
- auto_process_ngs.cli.auto_process.archive(args)
Implement functionality for ‘archive’ command
- auto_process_ngs.cli.auto_process.clone(args)
Implement functionality for ‘clone’ command
- auto_process_ngs.cli.auto_process.config(args)
Implement functionality for ‘config’ command
- auto_process_ngs.cli.auto_process.import_project(args)
Implement functionality for ‘import_project’ command
- auto_process_ngs.cli.auto_process.info(args)
Implement functionality for the ‘info’ command
- auto_process_ngs.cli.auto_process.main()
- auto_process_ngs.cli.auto_process.make_fastqs(args)
Implement functionality for ‘make_fastqs’ command
- auto_process_ngs.cli.auto_process.merge_fastq_dirs(args)
Implement functionality for ‘merge_fastq_dirs’ command
- auto_process_ngs.cli.auto_process.metadata(args)
Implement functionality for ‘metadata’ command
- auto_process_ngs.cli.auto_process.params(args)
Implement functionality for ‘params’ command
- auto_process_ngs.cli.auto_process.publish_qc(args)
Implement functionality for ‘publish_qc’ command
- auto_process_ngs.cli.auto_process.readme(args)
Implement functionality for ‘readme’ command
- auto_process_ngs.cli.auto_process.report(args)
Implement functionality for ‘report’ command
- auto_process_ngs.cli.auto_process.run_qc(args)
Implement functionality for ‘run_qc’ command
- auto_process_ngs.cli.auto_process.samplesheet(args)
Implement functionality for ‘samplesheet’ command
- auto_process_ngs.cli.auto_process.set_debug(debug_flag)
Turn on debug output
- auto_process_ngs.cli.auto_process.setup(args)
Implement functionality for ‘setup’ command
- auto_process_ngs.cli.auto_process.setup_analysis_dirs(args)
Implement functionality for ‘setup_analysis_dirs’ command
- auto_process_ngs.cli.auto_process.update(args)
Implement functionality for ‘update’ command
- auto_process_ngs.cli.auto_process.update_fastq_stats(args)
Implement functionality for ‘update_fastq_stats’ command