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branch: cgap_pipeline_updates

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• cgap_pipeline_updates
• CGAP_V16
• Data_Use_Guideline_Check
• FF-1006
• FF-1008
• FF-1009
• FF-1011
• FF-1013
• FF-1021
• FF-1022
• FF-1024
• FF-1026
• FF-1026_2
• FF-1030
• FF-1030_2
• FF-1033
• FF-1035
• FF-1036
• FF-1042
• FF-1043
• FF-1047
• FF-1047_2
• FF-1060
• FF-1061
• FF-1079
• FF-1084
• FF-1085
• FF-1086-from-tibanna
• FF-1087
• FF-1090
• FF-984
• FF-997
• FF-997_2
• FF-998
• MARGI-static-header
• MARGI_wfr
• Pipeline_spot_management
• V17-updates
• V17-updates-2
• V17-updates-3
• action_fix
• action_history
• add-description
• add-mount-for-cgap
• add-new-nz-files
• add-zebrafish-mboI
• add_bed_2_higlass_check
• add_cram_wf
• add_email_option_pending_lab
• add_mpileup_cgap_step1
• add_nz
• add_pipelines
• add_pipelines_2
• add_timeouts
• add_vistrack_2_hg_chk
• add_wait_starting_runs
• allow_action_fix
• assay_shortnames
• audits
• auth_hotfix
• auth_test_change
• autodoc
• automating_checks
• av/improve-higlass-registration
• badge_messages_array
• badges2
• badges_fxn
• bam_snap-update
• bamqc_benchmarking_fix
• bamqc_metrics_summary
• bamqc_timeout_fix
• bed2bedb_check_fixes
• bed2beddb_fix
• bedtobeddb_v3
• bedtomultivec
• berg_cgap_autodeploy
• berg_cgap_deploy_fix
• bg2bw_v5
• bgtobw
• biof_eng_const_fix
• biofeat_org_chk
• biorxiv2pub
• biosample_badges
• body_size_hotfix
• bs_badge_fix
• bs_badge_msglist
• bs_badges_envs
• build_check_fix
• build_indices_fix
• c4_161
• c4_314
• c4_58
• cache_removal
• cagp_obs_sugg
• case_fix
• cert
• cgap
• cgap-pipeline-updates-8
• cgap-v12
• cgapV16_updates
• cgap_PartI_WES
• cgap_add_error_report
• cgap_checks_updates
• cgap_fastqc_updates
• cgap_fix
• cgap_md5_fix
• cgap_multi_sample_analysis
• cgap_pipeline
• cgap_pipeline_2
• cgap_pipeline_updates_2
• cgap_pipeline_updates_3
• cgap_pipeline_updates_5
• cgap_pipeline_updates_6
• cgap_spot_off
• cgap_suggested_enum_fix
• cgap_v17
• change_in_item_counts_v2
• check-suggested-enum
• check_dbxrefs
• check_duplicate_opfs
• check_fastq_ids
• check_fixes
• check_hic_summary
• check_idx_higlass
• check_latest_wf_version
• check_opf_status_edit
• check_problematic_runs
• check_queries_fixes
• chk4track_meta
• chkbiorxiv4pub
• clean_old_s3
• cloudwatch_rules
• connection_refactor
• continious_staggering
• cypress_check_automation
• cypress_check_bug_fixes
• cypress_check_bug_fixes2
• daily_cron_fix
• data_release_grammar
• data_release_hack
• data_usage_status_edit
• dcicutils_0.4.0
• dedup
• dedup_round_2
• dedup_test
• default_values
• del_f_w_live_wfr
• delete_env
• delete_problematic_running_runs
• deploy_fix
• deploy_fixes
• deploys
• disable-converters
• disable_all_pipeline_runs
• docs
• docs_build
• don't-check-qc-on-step4
• dont_ingest_tag_cgapwolf
• dont_skip_small_sets
• doppelganger-add_user_created_items
• download_tracking
• downstream
• dt_processing_3_12_19
• ec2_wfr_info
• env_cgap
• enzyme_fix
• es6
• es_check
• eset_chg_track
• exp_type_rd2
• exptype_check_fix
• fastq_formatqc
• fastq_tar
• fastqc_new_versions
• fastqc_on_processed_files
• fetch_wfr_related_items
• ff_metrics
• file_processed
• files_not_registered_with_higlass
• filesize
• fix_auto_filesize
• fix_badge_redundancy
• fix_cgap_fastqc
• fix_higlass_chks
• fix_higlassupdate_expsets_otherprocessedfiles_error
• fix_long_run_name_error
• frag_size_edit
• fs_keys
• generate_view_configs
• good_badges
• google_utils_fix
• grouped_with_check
• header_checks
• hela_check
• help_url_check
• hic_pipeline_fix
• higlass-registration-local
• higlass_check_update
• higlass_checks
• higlass_file_act
• higlass_mins_leeway
• higlass_opf_fix
• higlass_patch_fix
• higlass_processed_file_combine
• higlass_processed_fix
• higlass_quickfix
• higlass_reg_fixes
• higlass_schema_changes
• higlass_uid_fix
• history_fix
• hot-pipeline-fix
• ignored_enum
• in_situ_chia_pet
• indexing_progress
• indexing_records_fix
• ingestion_trigger
• insulation_scores_and_boundaries_pipeline
• insulator_score_pipeline
• investigate_check_delay
• json
• json_fix
• kill_ec2_action
• kmp_C4-95_env_utils_leftover_issues
• kmp_C4-95_use_utils_0-10-0
• lab_opfs
• limit_all_hotfix
• login_redirect
• madqc
• margi_bams
• margi_fix_wfr_version
• margi_qc_metric_summary_and_enzyme_check
• margi_quality_metric_summary
• margi_v4
• master
• md5_fastq_auto
• micro_c_official
• migrate_to_pytest
• misc_changes
• misc_fixes
• mismatch_info
• mod_biorxiv_chk
• mod_chk_timing
• monthly_rds
• more_higlass_checks
• new_chalice
• new_enzyme_patterns
• new_header_checks
• new_utils
• no_filesize
• no_pr_deploy
• ont_fix
• ontology_404
• ontology_updates
• opf_check_expand
• opf_status_check
• optimize
• partIII
• peddy_qc
• pending_users_check
• performance_check_tweak
• pipeline-updates
• pipelines-3
• placeholder_config
• pmid_geo_links
• poetry
• prod
• production
• purge_fix
• purge_search_res
• qc_metrics_list_fixes
• qc_update
• qctable
• qctable2
• qctable3
• qctable4
• query_string
• queue_action_envs
• queue_action_higlass
• queue_dedup_2
• quick_fixes
• re_check
• re_checker_update
• re_new_enzymes
• redirect_fix
• register-higlass
• register_higlass_v2
• rel_upd_chk
• release_updates_fix
• release_updates_notes
• release_updates_project
• rename_checks
• replicate_audit
• rm_cgap
• rna_seq_pipeline
• rna_strandedness_fixes
• rna_strandness
• rnaqc
• run_action_kwarg
• say_my_name
• schedule_fix
• sci_HiC-&-DNase_HiC
• security_fix
• soo
• staging_fix
• status_mismatch_chk
• subprocess
• summary_in_history
• sync_analytics
• testin
• time_dedup
• tweak_sched
• tweak_status_for_higlass_uuid_check
• up_timeout
• upd_biorxiv_chk
• upd_bioxriv_to_pub
• upd_chks_w_get_es
• upd_opf_s_mis
• upd_pending_lab_action
• update-brief-info-cgap-runs
• update-complete-tags
• update-indexing-status-on-capture-hic
• update_auth
• update_cgap_config
• update_fastqc_version
• update_url_check
• updates
• updates_cgap_pipeline
• url_escapes
• url_exceptions
• url_readtimeout
• url_timeout
• use_ff_keys
• use_query_search
• utils_026
• v11
• valid_gene_chk
• validation_errors_search
• various_small_features
• warning_badges
• webdev_check
• wf_version_check_fix
• wfr_indexing_status_check
• wipe_indices
• wolf_er
• workflow_audit
• wrangler_meeting
• zebra_fish_ref_files
• zfish_maxsize

Build # 3049

Build Type

Pull #332

travis-ci

Committed by web-flow

Commit Message

Merge b579c7db5 into 1f506fd9c

Pull Request Pull Request #332: cgap_pipeline_updates

Run Details

501 of 577 branches covered (86.83%)

Branch coverage included in aggregate %.

1285 of 1389 relevant lines covered (92.51%)

0.93 hits per line