Index

A

add_pseudo_lane_for_miseq() (igf_data.illumina.samplesheet.SampleSheet method) add_pseudo_lane_for_nextseq() (igf_data.illumina.samplesheet.SampleSheet method) add_seqrun_path_info() (in module igf_data.utils.project_data_display_utils)

Analysis (class in igf_data.igfdb.igfTables) Analysis_collection_utils (class in igf_data.utils.analysis_collection_utils) assign_user_to_project() (igf_data.igfdb.projectadaptor.ProjectAdaptor method)

B

BaseAdaptor (class in igf_data.igfdb.baseadaptor) BasesMask (class in igf_data.illumina.basesMask)

build_biodalliance_config() (igf_data.utils.config_genome_browser.Config_genome_browser method) BWA_util (class in igf_data.utils.tools.bwa_utils)

C

calculate_bases_mask() (igf_data.illumina.basesMask.BasesMask method) calculate_file_checksum() (in module igf_data.utils.fileutils) calculate_file_md5() (in module igf_data.process.seqrun_processing.find_and_process_new_seqrun) change_singlecell_barcodes() (igf_data.process.singlecell_seqrun.processsinglecellsamplesheet.ProcessSingleCellSamplesheet method) check_cellranger_count_output() (in module igf_data.utils.tools.cellranger.cellranger_count_utils) check_collection_attribute() (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) check_collection_records_name_and_type() (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) check_data_authority_for_project() (igf_data.igfdb.projectadaptor.ProjectAdaptor method) check_existing_project_user() (igf_data.igfdb.projectadaptor.ProjectAdaptor method) check_experiment_records_id() (igf_data.igfdb.experimentadaptor.ExperimentAdaptor method) check_file_path() (in module igf_data.utils.fileutils) check_file_records_file_path() (igf_data.igfdb.fileadaptor.FileAdaptor method) check_finished_seqrun_dir() (in module igf_data.process.seqrun_processing.find_and_process_new_seqrun) check_for_registered_project_and_sample() (in module igf_data.process.seqrun_processing.find_and_process_new_seqrun) check_metadata_library_by_row() (igf_data.utils.validation_check.metadata_validation.Validate_project_and_samplesheet_metadata static method) check_project_and_sample() (igf_data.igfdb.sampleadaptor.SampleAdaptor method) check_project_attributes() (igf_data.igfdb.projectadaptor.ProjectAdaptor method) check_project_records_igf_id() (igf_data.igfdb.projectadaptor.ProjectAdaptor method) check_run_records_igf_id() (igf_data.igfdb.runadaptor.RunAdaptor method) check_sample_header() (igf_data.illumina.samplesheet.SampleSheet method) check_sample_records_igf_id() (igf_data.igfdb.sampleadaptor.SampleAdaptor method) check_seed_id_status() (igf_data.igfdb.pipelineadaptor.PipelineAdaptor method) check_seqrun_dir_in_db() (in module igf_data.process.seqrun_processing.find_and_process_new_seqrun) check_seqrun_exists() (igf_data.igfdb.seqrunadaptor.SeqrunAdaptor method)

check_user_records_email_id() (igf_data.igfdb.useradaptor.UserAdaptor method) clean_and_rebuild_database() (in module igf_data.utils.dbutils) Collect_seqrun_fastq_to_db (class in igf_data.process.seqrun_processing.collect_seqrun_fastq_to_db) Collection (class in igf_data.igfdb.igfTables) Collection_attribute (class in igf_data.igfdb.igfTables) Collection_group (class in igf_data.igfdb.igfTables) CollectionAdaptor (class in igf_data.igfdb.collectionadaptor) compare_fastq_files_read_counts() (in module igf_data.utils.fastq_utils) compare_metadata() (igf_data.utils.validation_check.metadata_validation.Validate_project_and_samplesheet_metadata method) Config_genome_browser (class in igf_data.utils.config_genome_browser) convert_bam_to_cram() (in module igf_data.utils.tools.samtools_utils), [1] convert_errors_to_gviz() (igf_data.utils.validation_check.metadata_validation.Validate_project_and_samplesheet_metadata method) convert_project_data_gviz_data() (in module igf_data.utils.project_data_display_utils) convert_to_gviz_json_for_display() (in module igf_data.utils.gviz_utils) copy_bcl_files() (igf_data.process.moveBclFilesForDemultiplexing.moveBclTilesForDemultiplexing method) copy_local_file() (in module igf_data.utils.fileutils) copy_remote_file() (in module igf_data.utils.fileutils) count_fastq_lines() (in module igf_data.utils.fastq_utils) count_project_samples() (igf_data.igfdb.projectadaptor.ProjectAdaptor method) create_collection_group() (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) create_file_manifest_for_dir() (in module igf_data.utils.fileutils) create_or_update_analysis_collection() (igf_data.utils.analysis_collection_utils.Analysis_collection_utils method) create_or_update_collection_attributes() (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) create_pipeline_seed() (igf_data.igfdb.pipelineadaptor.PipelineAdaptor method)

D

detect_non_fastq_in_file_list() (in module igf_data.utils.fastq_utils) divide_data_to_table_and_attribute() (igf_data.igfdb.baseadaptor.BaseAdaptor method) (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) (igf_data.igfdb.experimentadaptor.ExperimentAdaptor method) (igf_data.igfdb.fileadaptor.FileAdaptor method) (igf_data.igfdb.projectadaptor.ProjectAdaptor method) (igf_data.igfdb.runadaptor.RunAdaptor method) (igf_data.igfdb.sampleadaptor.SampleAdaptor method) (igf_data.igfdb.seqrunadaptor.SeqrunAdaptor method)

draft_email_for_project_cleanup() (in module igf_data.utils.projectutils) dump_error_to_csv() (igf_data.utils.validation_check.metadata_validation.Validate_project_and_samplesheet_metadata method)

E

Experiment (class in igf_data.igfdb.igfTables) Experiment_attribute (class in igf_data.igfdb.igfTables)

Experiment_metadata_updator (class in igf_data.process.metadata.experiment_metadata_updator) ExperimentAdaptor (class in igf_data.igfdb.experimentadaptor) extract_cellranger_count_metrics_summary() (in module igf_data.utils.tools.cellranger.cellranger_count_utils)

F

Fastp_utils (class in igf_data.utils.tools.fastp_utils) fetch_all_project_igf_ids() (igf_data.igfdb.projectadaptor.ProjectAdaptor method) fetch_collection_name_and_table_from_file_path() (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) fetch_collection_records_name_and_type() (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) fetch_data_authority_for_project() (igf_data.igfdb.projectadaptor.ProjectAdaptor method) fetch_experiment_records_id() (igf_data.igfdb.experimentadaptor.ExperimentAdaptor method) fetch_file_records_file_path() (igf_data.igfdb.fileadaptor.FileAdaptor method) fetch_flowcell_and_lane_for_run() (igf_data.igfdb.runadaptor.RunAdaptor method) fetch_flowcell_barcode_rules_for_seqrun() (igf_data.igfdb.seqrunadaptor.SeqrunAdaptor method) fetch_pipeline_records_pipeline_name() (igf_data.igfdb.pipelineadaptor.PipelineAdaptor method) fetch_pipeline_seed() (igf_data.igfdb.pipelineadaptor.PipelineAdaptor method) fetch_pipeline_seed_with_table_data() (igf_data.igfdb.pipelineadaptor.PipelineAdaptor method) fetch_platform_info_for_seqrun() (igf_data.igfdb.seqrunadaptor.SeqrunAdaptor method) fetch_platform_records_igf_id() (igf_data.igfdb.platformadaptor.PlatformAdaptor method) fetch_project_and_sample_for_experiment() (igf_data.igfdb.experimentadaptor.ExperimentAdaptor method) fetch_project_records_igf_id() (igf_data.igfdb.projectadaptor.ProjectAdaptor method) fetch_project_sample_and_experiment_for_run() (igf_data.igfdb.runadaptor.RunAdaptor method) fetch_project_samples() (igf_data.igfdb.projectadaptor.ProjectAdaptor method) fetch_records() (igf_data.igfdb.baseadaptor.BaseAdaptor method) fetch_records_by_column() (igf_data.igfdb.baseadaptor.BaseAdaptor method) fetch_records_by_multiple_column() (igf_data.igfdb.baseadaptor.BaseAdaptor method)

fetch_run_records_igf_id() (igf_data.igfdb.runadaptor.RunAdaptor method) fetch_runs_for_igf_id() (igf_data.igfdb.experimentadaptor.ExperimentAdaptor method) fetch_sample_attribute_records_for_experiment_igf_id() (igf_data.igfdb.experimentadaptor.ExperimentAdaptor method) fetch_sample_info_for_run() (igf_data.igfdb.runadaptor.RunAdaptor method) fetch_sample_project() (igf_data.igfdb.sampleadaptor.SampleAdaptor method) fetch_sample_records_igf_id() (igf_data.igfdb.sampleadaptor.SampleAdaptor method) fetch_seqrun_and_platform_list_for_sample_id() (igf_data.igfdb.sampleadaptor.SampleAdaptor method) fetch_seqrun_records_igf_id() (igf_data.igfdb.seqrunadaptor.SeqrunAdaptor method) fetch_user_records_email_id() (igf_data.igfdb.useradaptor.UserAdaptor method) fetch_user_records_igf_id() (igf_data.igfdb.useradaptor.UserAdaptor method) File (class in igf_data.igfdb.igfTables) File_attribute (class in igf_data.igfdb.igfTables) FileAdaptor (class in igf_data.igfdb.fileadaptor) filter_bam_file() (in module igf_data.utils.tools.samtools_utils), [1] filter_sample_data() (igf_data.illumina.samplesheet.SampleSheet method) Find_and_register_new_project_data (class in igf_data.process.seqrun_processing.find_and_register_new_project_data) find_fastq_and_build_db_collection() (igf_data.process.seqrun_processing.collect_seqrun_fastq_to_db.Collect_seqrun_fastq_to_db method) find_new_analysis_seeds() (in module igf_data.utils.pipelineutils) find_new_seqrun_dir() (in module igf_data.process.seqrun_processing.find_and_process_new_seqrun) find_projects_for_cleanup() (in module igf_data.utils.projectutils) Flowcell_barcode_rule (class in igf_data.igfdb.igfTables)

G

GATK_tools (class in igf_data.utils.tools.gatk_utils) generate_aligned_bams() (igf_data.utils.tools.star_utils.Star_utils method) generate_gviz_json_file() (igf_data.utils.project_status_utils.Project_status method) generate_rna_bigwig() (igf_data.utils.tools.star_utils.Star_utils method) get_analysis_data_for_project() (igf_data.utils.project_analysis_utils.Project_analysis method) get_analysis_info() (igf_data.utils.project_status_utils.Project_status method) get_attributes_by_dbid() (igf_data.igfdb.baseadaptor.BaseAdaptor method) get_blacklist_region_bed() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_cellranger_count_input_list() (in module igf_data.utils.tools.cellranger.cellranger_count_utils) get_collection_files() (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) get_date_stamp() (in module igf_data.utils.fileutils) get_date_stamp_for_file_name() (in module igf_data.utils.fileutils) get_datestamp_label() (in module igf_data.utils.fileutils) get_dbsnp_vcf() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_fastq_and_run_for_samples() (in module igf_data.utils.analysis_fastq_fetch_utils) get_fastq_info_from_fastq_zip() (in module igf_data.utils.fastqc_utils) get_fastq_input_list() (in module igf_data.utils.analysis_fastq_fetch_utils) get_file_extension() (in module igf_data.utils.fileutils) get_files_and_irods_path_for_project() (in module igf_data.utils.projectutils) get_flowcell_name() (igf_data.illumina.runinfo_xml.RunInfo_xml method) get_gatk_indel_ref() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_gatk_snp_ref() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_gene_gtf() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_gene_reflat() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_generic_ref_files() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_genome_bowtie2() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_genome_bwa() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_genome_dict() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_genome_fasta() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_genome_fasta_fai() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_genome_minimap2() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_hiseq_flowcell() (igf_data.illumina.runparameters_xml.RunParameter_xml method)

get_index_count() (igf_data.illumina.samplesheet.SampleSheet method) get_indexes() (igf_data.illumina.samplesheet.SampleSheet method) get_lane_count() (igf_data.illumina.samplesheet.SampleSheet method) get_merged_errors() (igf_data.utils.validation_check.metadata_validation.Validate_project_and_samplesheet_metadata method) get_metadata_validation_report() (igf_data.utils.validation_check.metadata_validation.Validate_project_and_samplesheet_metadata method) get_new_file_name() (igf_data.utils.analysis_collection_utils.Analysis_collection_utils method) get_pipeline_seeds() (in module igf_data.utils.ehive_utils.pipeseedfactory_utils) get_platform_name() (igf_data.illumina.samplesheet.SampleSheet method) get_platform_number() (igf_data.illumina.runinfo_xml.RunInfo_xml method) get_project_and_lane() (igf_data.illumina.samplesheet.SampleSheet method) get_project_attributes() (igf_data.igfdb.projectadaptor.ProjectAdaptor method) get_project_names() (igf_data.illumina.samplesheet.SampleSheet method) get_project_read_count() (in module igf_data.utils.projectutils) get_project_user_info() (igf_data.igfdb.projectadaptor.ProjectAdaptor method) get_reads_stats() (igf_data.illumina.runinfo_xml.RunInfo_xml method) get_reverse_complement_index() (igf_data.illumina.samplesheet.SampleSheet method) get_ribosomal_interval() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_samplesheet_validation_report() (igf_data.utils.validation_check.metadata_validation.Validate_project_and_samplesheet_metadata method) get_seqrun_date_from_igf_id() (in module igf_data.utils.seqrunutils) get_seqrun_info() (igf_data.utils.project_status_utils.Project_status method) get_seqrun_info_for_project() (in module igf_data.utils.projectutils) get_status_column_order() (igf_data.utils.project_status_utils.Project_status static method) get_status_description() (igf_data.utils.project_status_utils.Project_status static method) get_storage_stats_in_gb() (in module igf_data.utils.disk_usage_utils) get_sub_directory_size_in_gb() (in module igf_data.utils.disk_usage_utils) get_table_columns() (igf_data.igfdb.baseadaptor.BaseAdaptor method) get_temp_dir() (in module igf_data.utils.fileutils) get_transcriptome_rsem() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_transcriptome_star() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_transcriptome_tenx() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) get_twobit_genome_url() (igf_data.utils.tools.reference_genome_utils.Reference_genome_utils method) group_data_by_index_length() (igf_data.illumina.samplesheet.SampleSheet method)

H

History (class in igf_data.igfdb.igfTables)

I

identify_fastq_pair() (in module igf_data.utils.fastq_utils) igf_data.igfdb.baseadaptor module igf_data.igfdb.collectionadaptor module igf_data.igfdb.experimentadaptor module igf_data.igfdb.fileadaptor module igf_data.igfdb.igfTables module igf_data.igfdb.pipelineadaptor module igf_data.igfdb.platformadaptor module igf_data.igfdb.projectadaptor module igf_data.igfdb.runadaptor module igf_data.igfdb.sampleadaptor module igf_data.igfdb.seqrunadaptor module igf_data.igfdb.useradaptor module igf_data.illumina.basesMask module igf_data.illumina.runinfo_xml module igf_data.illumina.runparameters_xml module igf_data.illumina.samplesheet module igf_data.process.metadata.experiment_metadata_updator module igf_data.process.moveBclFilesForDemultiplexing module igf_data.process.pipeline.modify_pipeline_seed module igf_data.process.seqrun_processing.collect_seqrun_fastq_to_db module igf_data.process.seqrun_processing.find_and_process_new_seqrun module igf_data.process.seqrun_processing.find_and_register_new_project_data module igf_data.process.seqrun_processing.reset_samplesheet_md5 module igf_data.process.singlecell_seqrun.mergesinglecellfastq module igf_data.process.singlecell_seqrun.processsinglecellsamplesheet module igf_data.utils.analysis_fastq_fetch_utils module igf_data.utils.config_genome_browser module

igf_data.utils.dbutils module igf_data.utils.disk_usage_utils module igf_data.utils.ehive_utils.pipeseedfactory_utils module igf_data.utils.fastq_utils module igf_data.utils.fastqc_utils module igf_data.utils.fileutils module igf_data.utils.gviz_utils module igf_data.utils.igf_irods_client module igf_data.utils.pipelineutils module igf_data.utils.platformutils module igf_data.utils.project_analysis_utils module igf_data.utils.project_data_display_utils module igf_data.utils.project_status_utils module igf_data.utils.projectutils module igf_data.utils.seqrunutils module igf_data.utils.sequtils module igf_data.utils.tools.bwa_utils module igf_data.utils.tools.cellranger.cellranger_count_utils module igf_data.utils.tools.fastp_utils module igf_data.utils.tools.gatk_utils module igf_data.utils.tools.picard_util module igf_data.utils.tools.reference_genome_utils module igf_data.utils.tools.rsem_utils module igf_data.utils.tools.samtools_utils module, [1] igf_data.utils.tools.star_utils module igf_data.utils.tools.subread_utils module igf_data.utils.validation_check.metadata_validation module IGF_irods_uploader (class in igf_data.utils.igf_irods_client) index_bam_or_cram() (in module igf_data.utils.tools.samtools_utils), [1]

L

list_remote_file_or_dirs() (in module igf_data.utils.fileutils) load_file_and_create_collection() (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) load_file_to_disk_and_db() (igf_data.utils.analysis_collection_utils.Analysis_collection_utils method) load_new_flowcell_data() (in module igf_data.utils.platformutils)

load_new_pipeline_data() (in module igf_data.utils.pipelineutils) load_new_platform_data() (in module igf_data.utils.platformutils) load_new_seqrun_data() (in module igf_data.utils.seqrunutils) load_seqrun_files_to_db() (in module igf_data.process.seqrun_processing.find_and_process_new_seqrun)

M

map_foreign_table_and_store_attribute() (igf_data.igfdb.baseadaptor.BaseAdaptor method) mark_project_and_list_files_for_cleanup() (in module igf_data.utils.projectutils) mark_project_as_withdrawn() (in module igf_data.utils.projectutils) mark_project_barcode_check_off() (in module igf_data.utils.projectutils) merge_fastq_per_lane_per_sample() (igf_data.process.singlecell_seqrun.mergesinglecellfastq.MergeSingleCellFastq method) merge_multiple_bam() (in module igf_data.utils.tools.samtools_utils), [1] merge_storage_stats_json() (in module igf_data.utils.disk_usage_utils) MergeSingleCellFastq (class in igf_data.process.singlecell_seqrun.mergesinglecellfastq) Modify_pipeline_seed (class in igf_data.process.pipeline.modify_pipeline_seed) modify_sample_header() (igf_data.illumina.samplesheet.SampleSheet method) modify_samplesheet_for_sc_dual_barcode() (igf_data.process.singlecell_seqrun.processsinglecellsamplesheet.ProcessSingleCellDualIndexSamplesheet method) module igf_data.igfdb.baseadaptor igf_data.igfdb.collectionadaptor igf_data.igfdb.experimentadaptor igf_data.igfdb.fileadaptor igf_data.igfdb.igfTables igf_data.igfdb.pipelineadaptor igf_data.igfdb.platformadaptor igf_data.igfdb.projectadaptor igf_data.igfdb.runadaptor igf_data.igfdb.sampleadaptor igf_data.igfdb.seqrunadaptor igf_data.igfdb.useradaptor igf_data.illumina.basesMask igf_data.illumina.runinfo_xml igf_data.illumina.runparameters_xml igf_data.illumina.samplesheet igf_data.process.metadata.experiment_metadata_updator igf_data.process.moveBclFilesForDemultiplexing igf_data.process.pipeline.modify_pipeline_seed igf_data.process.seqrun_processing.collect_seqrun_fastq_to_db igf_data.process.seqrun_processing.find_and_process_new_seqrun igf_data.process.seqrun_processing.find_and_register_new_project_data igf_data.process.seqrun_processing.reset_samplesheet_md5 igf_data.process.singlecell_seqrun.mergesinglecellfastq igf_data.process.singlecell_seqrun.processsinglecellsamplesheet igf_data.utils.analysis_fastq_fetch_utils igf_data.utils.config_genome_browser igf_data.utils.dbutils igf_data.utils.disk_usage_utils igf_data.utils.ehive_utils.pipeseedfactory_utils igf_data.utils.fastq_utils igf_data.utils.fastqc_utils igf_data.utils.fileutils igf_data.utils.gviz_utils igf_data.utils.igf_irods_client igf_data.utils.pipelineutils igf_data.utils.platformutils igf_data.utils.project_analysis_utils igf_data.utils.project_data_display_utils igf_data.utils.project_status_utils igf_data.utils.projectutils igf_data.utils.seqrunutils igf_data.utils.sequtils igf_data.utils.tools.bwa_utils igf_data.utils.tools.cellranger.cellranger_count_utils igf_data.utils.tools.fastp_utils igf_data.utils.tools.gatk_utils igf_data.utils.tools.picard_util igf_data.utils.tools.reference_genome_utils igf_data.utils.tools.rsem_utils igf_data.utils.tools.samtools_utils, [1] igf_data.utils.tools.star_utils igf_data.utils.tools.subread_utils igf_data.utils.validation_check.metadata_validation

move_file() (in module igf_data.utils.fileutils) moveBclTilesForDemultiplexing (class in igf_data.process.moveBclFilesForDemultiplexing)

N

notify_project_for_cleanup() (in module igf_data.utils.projectutils)

P

Picard_tools (class in igf_data.utils.tools.picard_util) Pipeline (class in igf_data.igfdb.igfTables) Pipeline_seed (class in igf_data.igfdb.igfTables) PipelineAdaptor (class in igf_data.igfdb.pipelineadaptor) Platform (class in igf_data.igfdb.igfTables) PlatformAdaptor (class in igf_data.igfdb.platformadaptor) prepare_data_for_collection_attribute() (igf_data.igfdb.collectionadaptor.CollectionAdaptor static method) prepare_file_archive() (in module igf_data.utils.fileutils) prepare_seqrun_for_db() (in module igf_data.process.seqrun_processing.find_and_process_new_seqrun) preprocess_path_name() (in module igf_data.utils.fileutils)

print_sampleSheet() (igf_data.illumina.samplesheet.SampleSheet method) process_project_data_and_account() (igf_data.process.seqrun_processing.find_and_register_new_project_data.Find_and_register_new_project_data method) ProcessSingleCellDualIndexSamplesheet (class in igf_data.process.singlecell_seqrun.processsinglecellsamplesheet) ProcessSingleCellSamplesheet (class in igf_data.process.singlecell_seqrun.processsinglecellsamplesheet) Project (class in igf_data.igfdb.igfTables) Project_analysis (class in igf_data.utils.project_analysis_utils) Project_attribute (class in igf_data.igfdb.igfTables) Project_status (class in igf_data.utils.project_status_utils) ProjectAdaptor (class in igf_data.igfdb.projectadaptor) ProjectUser (class in igf_data.igfdb.igfTables)

R

read_dbconf_json() (in module igf_data.utils.dbutils) read_json_data() (in module igf_data.utils.dbutils) (in module igf_data.utils.fileutils) Reference_genome_utils (class in igf_data.utils.tools.reference_genome_utils) remove_collection_group_info() (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) remove_dir() (in module igf_data.utils.fileutils) remove_file_data_for_file_path() (igf_data.igfdb.fileadaptor.FileAdaptor method) reset_pipeline_seed_for_rerun() (igf_data.process.pipeline.modify_pipeline_seed.Modify_pipeline_seed method) Reset_samplesheet_md5 (class in igf_data.process.seqrun_processing.reset_samplesheet_md5) rev_comp() (in module igf_data.utils.sequtils) RSEM_utils (class in igf_data.utils.tools.rsem_utils) Run (class in igf_data.igfdb.igfTables) run() (igf_data.process.seqrun_processing.reset_samplesheet_md5.Reset_samplesheet_md5 method) run_adapter_trimming() (igf_data.utils.tools.fastp_utils.Fastp_utils method) run_AnalyzeCovariates() (igf_data.utils.tools.gatk_utils.GATK_tools method) run_ApplyBQSR() (igf_data.utils.tools.gatk_utils.GATK_tools method)

Run_attribute (class in igf_data.igfdb.igfTables) run_bam_flagstat() (in module igf_data.utils.tools.samtools_utils), [1] run_bam_idxstat() (in module igf_data.utils.tools.samtools_utils), [1] run_bam_stats() (in module igf_data.utils.tools.samtools_utils), [1] run_BaseRecalibrator() (igf_data.utils.tools.gatk_utils.GATK_tools method) run_cellranger_multi() (in module igf_data.utils.tools.cellranger.cellranger_count_utils) run_featureCounts() (in module igf_data.utils.tools.subread_utils) run_HaplotypeCaller() (igf_data.utils.tools.gatk_utils.GATK_tools method) run_mem() (igf_data.utils.tools.bwa_utils.BWA_util method) run_picard_command() (igf_data.utils.tools.picard_util.Picard_tools method) run_rsem_calculate_expression() (igf_data.utils.tools.rsem_utils.RSEM_utils method) run_samtools_view() (in module igf_data.utils.tools.samtools_utils), [1] run_sort_bam() (in module igf_data.utils.tools.samtools_utils), [1] RunAdaptor (class in igf_data.igfdb.runadaptor) RunInfo_xml (class in igf_data.illumina.runinfo_xml) RunParameter_xml (class in igf_data.illumina.runparameters_xml)

S

Sample (class in igf_data.igfdb.igfTables) Sample_attribute (class in igf_data.igfdb.igfTables) SampleAdaptor (class in igf_data.igfdb.sampleadaptor) SampleSheet (class in igf_data.illumina.samplesheet) seed_new_experiments() (igf_data.igfdb.pipelineadaptor.PipelineAdaptor method) seed_new_seqruns() (igf_data.igfdb.pipelineadaptor.PipelineAdaptor method) seed_pipeline_table_for_new_seqrun() (in module igf_data.process.seqrun_processing.find_and_process_new_seqrun) send_email_to_user_via_sendmail() (in module igf_data.utils.projectutils) Seqrun (class in igf_data.igfdb.igfTables) Seqrun_attribute (class in igf_data.igfdb.igfTables) Seqrun_stats (class in igf_data.igfdb.igfTables) SeqrunAdaptor (class in igf_data.igfdb.seqrunadaptor) Star_utils (class in igf_data.utils.tools.star_utils) store_attributes() (igf_data.igfdb.baseadaptor.BaseAdaptor method) store_collection_and_attribute_data() (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) store_collection_attributes() (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) store_collection_data() (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) store_experiment_attributes() (igf_data.igfdb.experimentadaptor.ExperimentAdaptor method) store_experiment_data() (igf_data.igfdb.experimentadaptor.ExperimentAdaptor method) store_file_and_attribute_data() (igf_data.igfdb.fileadaptor.FileAdaptor method)

store_file_attributes() (igf_data.igfdb.fileadaptor.FileAdaptor method) store_file_data() (igf_data.igfdb.fileadaptor.FileAdaptor method) store_flowcell_barcode_rule() (igf_data.igfdb.platformadaptor.PlatformAdaptor method) store_pipeline_data() (igf_data.igfdb.pipelineadaptor.PipelineAdaptor method) store_platform_data() (igf_data.igfdb.platformadaptor.PlatformAdaptor method) store_project_and_attribute_data() (igf_data.igfdb.experimentadaptor.ExperimentAdaptor method) (igf_data.igfdb.projectadaptor.ProjectAdaptor method) store_project_attributes() (igf_data.igfdb.projectadaptor.ProjectAdaptor method) store_project_data() (igf_data.igfdb.projectadaptor.ProjectAdaptor method) store_records() (igf_data.igfdb.baseadaptor.BaseAdaptor method) store_run_and_attribute_data() (igf_data.igfdb.runadaptor.RunAdaptor method) store_run_attributes() (igf_data.igfdb.runadaptor.RunAdaptor method) store_run_data() (igf_data.igfdb.runadaptor.RunAdaptor method) store_sample_and_attribute_data() (igf_data.igfdb.sampleadaptor.SampleAdaptor method) store_sample_attributes() (igf_data.igfdb.sampleadaptor.SampleAdaptor method) store_sample_data() (igf_data.igfdb.sampleadaptor.SampleAdaptor method) store_seqrun_and_attribute_data() (igf_data.igfdb.seqrunadaptor.SeqrunAdaptor method) store_seqrun_attributes() (igf_data.igfdb.seqrunadaptor.SeqrunAdaptor method) store_seqrun_data() (igf_data.igfdb.seqrunadaptor.SeqrunAdaptor method) store_seqrun_stats_data() (igf_data.igfdb.seqrunadaptor.SeqrunAdaptor method) store_user_data() (igf_data.igfdb.useradaptor.UserAdaptor method)

U

update_collection_attribute() (igf_data.igfdb.collectionadaptor.CollectionAdaptor method) update_experiment_records_by_igf_id() (igf_data.igfdb.experimentadaptor.ExperimentAdaptor method) update_file_table_for_file_path() (igf_data.igfdb.fileadaptor.FileAdaptor method) update_metadta_from_sample_attribute() (igf_data.process.metadata.experiment_metadata_updator.Experiment_metadata_updator method)

update_pipeline_seed() (igf_data.igfdb.pipelineadaptor.PipelineAdaptor method) upload_analysis_results_and_create_collection() (igf_data.utils.igf_irods_client.IGF_irods_uploader method) upload_fastqfile_and_create_collection() (igf_data.utils.igf_irods_client.IGF_irods_uploader method) User (class in igf_data.igfdb.igfTables) UserAdaptor (class in igf_data.igfdb.useradaptor)

V

validate_metadata_library_type() (igf_data.utils.validation_check.metadata_validation.Validate_project_and_samplesheet_metadata static method) Validate_project_and_samplesheet_metadata (class in igf_data.utils.validation_check.metadata_validation)

validate_samplesheet_data() (igf_data.illumina.samplesheet.SampleSheet method) validate_samplesheet_for_seqrun() (in module igf_data.process.seqrun_processing.find_and_process_new_seqrun)