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