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Index
A
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B
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C
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D
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E
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F
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G
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I
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L
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M
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N
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P
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R
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S
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T
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U
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V
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W
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Y
A
add_contributing_lab_opf() (in module chalicelib.checks.wrangler_checks)
add_suggested_enum_values() (in module chalicelib.checks.wrangler_checks)
add_to_report() (in module chalicelib.checks.release_updates_checks)
add_viewconf_static_content_to_file() (in module chalicelib.checks.higlass_checks)
atac_seq_start() (in module chalicelib.checks.wfr_checks)
atac_seq_status() (in module chalicelib.checks.wfr_checks)
B
bam_re_start() (in module chalicelib.checks.wfr_checks)
bam_re_status() (in module chalicelib.checks.wfr_checks)
bamqc_start() (in module chalicelib.checks.wfr_checks)
bamqc_status() (in module chalicelib.checks.wfr_checks)
bed2beddb_start() (in module chalicelib.checks.wfr_checks)
bed2beddb_status() (in module chalicelib.checks.wfr_checks)
bed2multivec_start() (in module chalicelib.checks.wfr_checks)
bed2multivec_status() (in module chalicelib.checks.wfr_checks)
bg2bw_start() (in module chalicelib.checks.wfr_checks)
bg2bw_status() (in module chalicelib.checks.wfr_checks)
biorxiv_is_now_published() (in module chalicelib.checks.wrangler_checks)
biosource_cell_line_value() (in module chalicelib.checks.audit_checks)
C
capture_hic_start() (in module chalicelib.checks.wfr_checks)
capture_hic_status() (in module chalicelib.checks.wfr_checks)
chalicelib.checks.audit_checks (module)
chalicelib.checks.badge_checks (module)
chalicelib.checks.es_checks (module)
chalicelib.checks.header_checks (module)
chalicelib.checks.higlass_checks (module)
chalicelib.checks.release_updates_checks (module)
chalicelib.checks.system_checks (module)
chalicelib.checks.wfr_checks (module)
chalicelib.checks.wrangler_checks (module)
check_bio_feature_organism_name() (in module chalicelib.checks.audit_checks)
check_expsets_otherprocessedfiles_for_new_higlass_items() (in module chalicelib.checks.higlass_checks)
check_expsets_otherprocessedfiles_for_queried_files() (in module chalicelib.checks.higlass_checks)
check_expsets_processedfiles_for_modified_higlass_items() (in module chalicelib.checks.higlass_checks)
check_expsets_processedfiles_for_new_higlass_items() (in module chalicelib.checks.higlass_checks)
check_expsets_processedfiles_for_queried_higlass_items() (in module chalicelib.checks.higlass_checks)
check_external_references_uri() (in module chalicelib.checks.wrangler_checks)
check_fastq_read_id() (in module chalicelib.checks.audit_checks)
check_for_ontology_updates() (in module chalicelib.checks.wrangler_checks)
check_hic_summary_tables() (in module chalicelib.checks.wrangler_checks)
check_higlass_items_for_modified_files() (in module chalicelib.checks.higlass_checks)
check_higlass_items_for_new_files() (in module chalicelib.checks.higlass_checks)
check_higlass_items_for_queried_files() (in module chalicelib.checks.higlass_checks)
check_long_running_ec2s() (in module chalicelib.checks.system_checks)
check_opf_lab_different_than_experiment() (in module chalicelib.checks.wrangler_checks)
check_opf_status_mismatch() (in module chalicelib.checks.audit_checks)
check_search_urls() (in module chalicelib.checks.audit_checks)
check_suggested_enum_values() (in module chalicelib.checks.wrangler_checks)
check_validation_errors() (in module chalicelib.checks.audit_checks)
chia_pet_start() (in module chalicelib.checks.wfr_checks)
chia_pet_status() (in module chalicelib.checks.wfr_checks)
chip_seq_start() (in module chalicelib.checks.wfr_checks)
chip_seq_status() (in module chalicelib.checks.wfr_checks)
clean_s3_es_checks() (in module chalicelib.checks.es_checks)
clean_up_travis_queues() (in module chalicelib.checks.system_checks)
compare_badges() (in module chalicelib.checks.badge_checks)
compare_badges_and_messages() (in module chalicelib.checks.badge_checks)
compartments_caller_start() (in module chalicelib.checks.wfr_checks)
compartments_caller_status() (in module chalicelib.checks.wfr_checks)
consistent_replicate_info() (in module chalicelib.checks.badge_checks)
convert_es_timestamp_to_datetime() (in module chalicelib.checks.higlass_checks)
create_higlass_items_for_files() (in module chalicelib.checks.higlass_checks)
create_or_update_higlass_item() (in module chalicelib.checks.higlass_checks)
D
data_release_updates() (in module chalicelib.checks.release_updates_checks)
dilution_hic_start() (in module chalicelib.checks.wfr_checks)
dilution_hic_status() (in module chalicelib.checks.wfr_checks)
dnase_hic_start() (in module chalicelib.checks.wfr_checks)
dnase_hic_status() (in module chalicelib.checks.wfr_checks)
E
elastic_search_space() (in module chalicelib.checks.system_checks)
elasticsearch_s3_count_diff() (in module chalicelib.checks.es_checks)
exp_has_raw_files() (in module chalicelib.checks.badge_checks)
experiment_set_reporting_data() (in module chalicelib.checks.release_updates_checks)
expset_opf_unique_files() (in module chalicelib.checks.audit_checks)
expset_opf_unique_files_in_experiments() (in module chalicelib.checks.audit_checks)
expset_opfsets_unique_titles() (in module chalicelib.checks.audit_checks)
external_expsets_without_pub() (in module chalicelib.checks.audit_checks)
external_submission_but_missing_dbxrefs() (in module chalicelib.checks.audit_checks)
F
fastq_first_line_start() (in module chalicelib.checks.wfr_checks)
fastqc_start() (in module chalicelib.checks.wfr_checks)
fastqc_status() (in module chalicelib.checks.wfr_checks)
files_not_registered_with_higlass() (in module chalicelib.checks.higlass_checks)
find_cypress_test_items_to_purge() (in module chalicelib.checks.higlass_checks)
find_expsets_otherprocessedfiles_requiring_higlass_items() (in module chalicelib.checks.higlass_checks)
find_expsets_processedfiles_requiring_higlass_items() (in module chalicelib.checks.higlass_checks)
find_files_requiring_higlass_items() (in module chalicelib.checks.higlass_checks)
find_item_title() (in module chalicelib.checks.release_updates_checks)
find_items_for_header_processing() (in module chalicelib.checks.header_checks)
find_replacing_item() (in module chalicelib.checks.release_updates_checks)
G
gather_processedfiles_for_expset() (in module chalicelib.checks.higlass_checks)
generate_exp_set_report() (in module chalicelib.checks.release_updates_checks)
get_biorxiv_meta() (in module chalicelib.checks.wrangler_checks)
get_reference_files() (in module chalicelib.checks.higlass_checks)
get_viewconf_status() (in module chalicelib.checks.higlass_checks)
gold_biosamples() (in module chalicelib.checks.badge_checks)
grouped_with_file_relation_consistency() (in module chalicelib.checks.wrangler_checks)
I
in_situ_chia_pet_start() (in module chalicelib.checks.wfr_checks)
in_situ_chia_pet_status() (in module chalicelib.checks.wfr_checks)
in_situ_hic_start() (in module chalicelib.checks.wfr_checks)
in_situ_hic_status() (in module chalicelib.checks.wfr_checks)
insulation_scores_and_boundaries_start() (in module chalicelib.checks.wfr_checks)
insulation_scores_and_boundaries_status() (in module chalicelib.checks.wfr_checks)
interpolate_query_check_timestamps() (in module chalicelib.checks.higlass_checks)
L
long_running_wfrs_fdn_start() (in module chalicelib.checks.wfr_checks)
long_running_wfrs_fdn_status() (in module chalicelib.checks.wfr_checks)
M
margi_start() (in module chalicelib.checks.wfr_checks)
margi_status() (in module chalicelib.checks.wfr_checks)
md5run_start() (in module chalicelib.checks.wfr_checks)
md5run_status() (in module chalicelib.checks.wfr_checks)
md5run_status_extra_file() (in module chalicelib.checks.wfr_checks)
micro_c_start() (in module chalicelib.checks.wfr_checks)
micro_c_status() (in module chalicelib.checks.wfr_checks)
migrate_checks_to_es() (in module chalicelib.checks.es_checks)
N
nad_seq_start() (in module chalicelib.checks.wfr_checks)
nad_seq_status() (in module chalicelib.checks.wfr_checks)
new_or_updated_items() (in module chalicelib.checks.wrangler_checks)
P
paired_end_info_consistent() (in module chalicelib.checks.audit_checks)
pairsqc_start() (in module chalicelib.checks.wfr_checks)
pairsqc_status() (in module chalicelib.checks.wfr_checks)
patch_badges() (in module chalicelib.checks.badge_checks)
patch_expsets_otherprocessedfiles_for_new_higlass_items() (in module chalicelib.checks.higlass_checks)
patch_expsets_otherprocessedfiles_for_queried_files() (in module chalicelib.checks.higlass_checks)
patch_expsets_processedfiles_for_modified_higlass_items() (in module chalicelib.checks.higlass_checks)
patch_expsets_processedfiles_for_new_higlass_items() (in module chalicelib.checks.higlass_checks)
patch_expsets_processedfiles_for_queried_higlass_items() (in module chalicelib.checks.higlass_checks)
patch_file_higlass_uid() (in module chalicelib.checks.higlass_checks)
patch_hic_summary_tables() (in module chalicelib.checks.wrangler_checks)
patch_higlass_items_for_modified_files() (in module chalicelib.checks.higlass_checks)
patch_higlass_items_for_new_files() (in module chalicelib.checks.higlass_checks)
patch_higlass_items_for_queried_files() (in module chalicelib.checks.higlass_checks)
patch_items_with_headers() (in module chalicelib.checks.header_checks)
patch_strandedness_consistency_info() (in module chalicelib.checks.wrangler_checks)
plac_seq_start() (in module chalicelib.checks.wfr_checks)
plac_seq_status() (in module chalicelib.checks.wfr_checks)
post_viewconf_to_visualization_endpoint() (in module chalicelib.checks.higlass_checks)
problematic_wfrs_fdn_start() (in module chalicelib.checks.wfr_checks)
problematic_wfrs_fdn_status() (in module chalicelib.checks.wfr_checks)
process_download_tracking_items() (in module chalicelib.checks.system_checks)
publish_data_release_updates() (in module chalicelib.checks.release_updates_checks)
purge_cypress_items() (in module chalicelib.checks.higlass_checks)
purge_download_tracking_items() (in module chalicelib.checks.system_checks)
R
released_hela_files() (in module chalicelib.checks.audit_checks)
released_output_from_restricted_input() (in module chalicelib.checks.audit_checks)
repli_2_stage_start() (in module chalicelib.checks.wfr_checks)
repli_2_stage_status() (in module chalicelib.checks.wfr_checks)
repli_multi_stage_start() (in module chalicelib.checks.wfr_checks)
repli_multi_stage_status() (in module chalicelib.checks.wfr_checks)
repsets_have_bio_reps() (in module chalicelib.checks.badge_checks)
restrict_hela() (in module chalicelib.checks.audit_checks)
rna_seq_start() (in module chalicelib.checks.wfr_checks)
rna_seq_status() (in module chalicelib.checks.wfr_checks)
rna_strandedness_start() (in module chalicelib.checks.wfr_checks)
rna_strandedness_status() (in module chalicelib.checks.wfr_checks)
S
say_my_name() (in module chalicelib.checks.system_checks)
sync_google_analytics_data() (in module chalicelib.checks.release_updates_checks)
T
tcc_start() (in module chalicelib.checks.wfr_checks)
tcc_status() (in module chalicelib.checks.wfr_checks)
template_start() (in module chalicelib.checks.wfr_checks)
template_status() (in module chalicelib.checks.wfr_checks)
trac_loop_start() (in module chalicelib.checks.wfr_checks)
trac_loop_status() (in module chalicelib.checks.wfr_checks)
tsa_seq_start() (in module chalicelib.checks.wfr_checks)
tsa_seq_status() (in module chalicelib.checks.wfr_checks)
U
update_expsets_otherprocessedfiles_for_higlass_items() (in module chalicelib.checks.higlass_checks)
update_expsets_processedfiles_requiring_higlass_items() (in module chalicelib.checks.higlass_checks)
users_with_doppelganger() (in module chalicelib.checks.wrangler_checks)
users_with_pending_lab() (in module chalicelib.checks.wrangler_checks)
V
validate_entrez_geneids() (in module chalicelib.checks.wrangler_checks)
W
wipe_ff_build_indices() (in module chalicelib.checks.system_checks)
workflow_run_has_deleted_input_file() (in module chalicelib.checks.wrangler_checks)
Y
yellow_flag_biosamples() (in module chalicelib.checks.badge_checks)
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