biocore / mg-scripts

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• master
• TestFastQCJob
• add-tests
• add_assay_type
• add_callback
• add_fastq_annotation
• add_prep_info_file_gen
• add_replicate_method
• add_sif
• add_tellread
• amplicon_fixes
• amplicon_support2
• amplicon_support_hotfixes
• assay_type_verifier
• catch_all_zero_length
• changes-from-qiita-rc-10.2023
• config
• confirm_array_jobs_status
• copy_sequences
• dep_fix
• dynamic_gres
• errors_update
• extra_validation
• fastq_description_update
• fastqc
• fastqc_update
• filename_fix
• fix-sacct-array
• fix_katharoseq
• fix_read_csv
• fix_trimmed
• fixes-after-deploy-03.25
• gen-prep-fix
• get_sample_names
• get_sample_names_fix
• instrument_support
• job-arrays
• job_script_fix
• kraken2
• kraken2_revisited
• latest_fixes
• latest_updates
• loader_fix
• log_parsing
• metatranscriptomic_fix
• min_bytes=3.1K
• more_updates
• movi_day
• movi_updates
• multi_configuration
• multiqc_fix
• multiqc_inputs_fix
• multiqc_inputs_fix_re
• multiqc_update
• name_superset_fix
• new_polling_code
• nu_qc
• nu_qc_update
• output_filepaths
• perf_updates
• prepend_run_id_to_blanks
• prod_change
• prod_hotfixes
• prod_testing
• prod_updates
• production_fixes
• qiita_id
• qiita_id_fix
• qsub_fix
• rc_updates
• readd-dev_rm-SLURM_ARRAY_TASK_MIN
• real_world_test_fixes
• refactor
• refactor_output_folder
• refactor_outputs
• remove_default_profile
• remove_fastqc_node_constraint
• remove_vestigial
• replicate_validation_fix
• reserved_word_check
• restart_support
• revert-38-multiqc_inputs_fix
• rta_complete_check
• sample_sheet_names_fix
• sample_sheet_validation_hotfix
• sample_tracking
• sample_tracking3
• save-adapter-filtered
• seqcount_support
• seqpro
• seqpro_fix
• seqpro_refactor
• setup_update
• shm-se-changes
• sif_update
• slurm-1
• squeue_fixes
• support_plugin_refactoring
• support_replicates
• test_deploy
• test_updates
• testing_fixes
• trimmed_sequences_fix
• underscores_to_dots
• update_pipeline
• update_using_callback
• updates
• validation_fix
• wallclock_time_update
• with_pipeline_package
• wk-fixes

Build # 13710030712

Build Type

push

github

Committed by web-flow

Commit Message

fixes after deploy 03.25 (#169)

* Production hotfixes

* All tests are working

* Folded in MultiQCJob breakout PR (162)

* New files added

* Tests updated

* MultiQCJob updated

* Update sequence_processing_pipeline/MultiQCJob.py

Co-authored-by: Daniel McDonald <damcdonald@ucsd.edu>

* Update sequence_processing_pipeline/MultiQCJob.py

Co-authored-by: Daniel McDonald <damcdonald@ucsd.edu>

* Update sequence_processing_pipeline/MultiQCJob.py

Co-authored-by: Daniel McDonald <damcdonald@ucsd.edu>

* Updates based on feedback.

* Updates based on feedback

* Updates based on feedback

* address @wasade offset comment

* fixes after deploy 03.25

* self.commands -> self.array_cmds

* forgotten change

---------

Co-authored-by: Charles Cowart <ccowart@ucsd.edu>
Co-authored-by: Charles Cowart <42684307+charles-cowart@users.noreply.github.com>
Co-authored-by: Daniel McDonald <damcdonald@ucsd.edu>

Run Details

730 of 1181 branches covered (61.81%)

Branch coverage included in aggregate %.

15 of 17 new or added lines in 5 files covered. (88.24%)

4 existing lines in 1 file now uncovered.

2957 of 3438 relevant lines covered (86.01%)

0.86 hits per line