EdinburghGenomics / Analysis-Driver

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master: 80%

LAST BUILD ON BRANCH overwrite_tabix_bgzip

branch: overwrite_tabix_bgzip

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• overwrite_tabix_bgzip
• #374_include_coverage
• 231_bcl2fastq2.20
• 345_gatk4_trio_check
• 356_picard2.18
• 363_file_check
• 367_species_in_reporting
• 377_gatk4_pipeline
• 382_check_bcl_exists_for_cycle
• 385_deteminisic_samplesheet
• 390_pipeline_objects
• 394_limit_LIMS_rest_api
• 396_filter_qc
• 405_fix_IDT_barcode
• 408_add_gatk3.8
• 411_417_split_demultiplexing_per_lane
• 415_fix_fastqc
• Change_Sample_Ready_Requirements
• ContaminationCheck_KE
• Fix_gatk_genotype
• Link_Creation_Fix
• Release_0.26
• Release_v0.25.1
• Release_v0.25.2
• VB8_fix_execute
• VB8_validation_corrections
• align_run_elements
• asana_update
• bcbio_no_cleanup_integrationtest
• early_align_run_aborted
• early_alignment
• enforce_fastq_merge
• exception_in_main_proc
• faster_varcall_QC
• fastq_filterer_fixes
• fix_bcl2fastq
• fix_build
• fix_duplicated_unmapped
• fix_insert_sizes_type
• fix_integration_tests
• fix_lims_ntf
• fix_missing_gvcf
• fix_project_bug
• fix_run_element_mapping
• fix_run_qc
• gatk4
• genotype_gvcfs_memory
• integrate_lims
• integrate_lims2
• integration_test
• interop_metrics
• issue/231/bcl2fastq2.20
• load_output_conf
• master
• mwham_develop
• mwham_refactor
• nonhuman_variantcalling
• pdp_pool_fix
• project_on_valid_project
• project_process_MD5
• project_process_bugfix
• rapid_analysis
• record_data_source
• refactor
• relatedness_refactor
• remove_phix
• resume
• review_trigger
• sample_aggregate_defaults
• sample_datasets_fix
• sex
• test_gatk3.8
• tool_versions
• trios_relatedness
• update_core
• update_req_yield
• user_prep_libraries
• v0.17
• v0.18
• v0.18.1
• v0.19
• v0.19.1
• v0.19.2
• v0.20
• v0.20.1
• v0.21
• v0.22
• v0.22.1
• v0.23
• v0.23.1
• v0.24
• v0.24.1
• v0.25
• v0.25.1
• v0.25.2
• v0.25.3
• v0.26
• v0.26.1
• vb9_fixes

Build # 2180

Build Type

Pull #351

travis-ci

Committed by web-flow

Commit Message

make all tabix/bgzip command overwrite their output file if they exist already
Also refactor the commands to all use the same bash command generation.

Pull Request Pull Request #351: Overwrite with bgzip and tabix

Run Details

5 of 5 new or added lines in 2 files covered. (100.0%)

2467 of 3464 relevant lines covered (71.22%)

1.42 hits per line