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Staging for version 2.0#206

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Commits

Commits on Nov 7, 2019

• add rename and stats components

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• add remap hmmer component

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• remove converted tasks

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• move busco parsers to fileio submodule

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• convert and filter components

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• Add conversion components

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• Get gff3 merge command working

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• add busco, transdecoder wrappers

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• ADd annotate component

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• Merge branch 'decompose' of github.com:camillescott/dammit into decompose

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• add rename-transcriptome wrapper

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Commits on Nov 8, 2019

• add transdecoder test data, rules

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• add busco rule, busco testdata

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• add last

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• add infernal wrapper and rule

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Commits on Nov 13, 2019

• First round of workflow structuring: database download

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• merge download rules

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Commits on Nov 15, 2019

• add transdecoder, last, infernal, hmmer wrappers

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Commits on Nov 16, 2019

• init hmmer, transdecoder workflows

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Commits on Dec 2, 2019

• code removal

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• Merge branch 'decompose' of github.com:camillescott/dammit into decompose

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Commits on Dec 10, 2019

• add yaml; init annot snakes

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• init config changes; init main snake

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• yml db file

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Commits on Dec 12, 2019

• Merge branch 'decompose' of github.com:camillescott/dammit into decompose

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Commits on Dec 15, 2019

• working snakemake calls

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• fix md5 downloads

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• ignore metalink for now

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Commits on Dec 16, 2019

• fix lastdb wrapper

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• working transdecoder

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• getting... closer...

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• init env

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Commits on Feb 27, 2020

• Merge branch 'decompose' of github.com:camillescott/dammit into decompose

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• upd busco env and wrapper

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Commits on Feb 28, 2020

• Remove cruft; use paths relative to installation dir for config and workflows; add workflows and configs to MANIFEST

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• Merge branch 'decompose' of github.com:camillescott/dammit into decompose

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• Get annotate working with install-relative paths and fix some formatting in annotate workflow

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Commits on Apr 17, 2020

• Update requirements

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• init setup snakefile

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• Remove sphinx

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• Remove _build folder

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• add mkdocs to dev reqs

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• Merge pull request #171 from dib-lab/update_reqs

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Commits on Apr 18, 2020

• init file conversion rules

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• add gff3 file targets; fix rename txome wrapper

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• Merge pull request #175 from dib-lab/add_conversion_rules

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Commits on Apr 23, 2020

• init shmlast wrapper, init shmlast and busco-v4 rules

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Commits on Apr 24, 2020

• Refactor config and add config components

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• First pass unifying argparse and click interfaces

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• Add database dir as envvar

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• add .snakemake to gitignore

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• vendor cloup

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• Reorganize components into cloup groups

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• Remove busco tasks

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• remove tasks suybmodules

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  0c3f2d8

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• Fix regression in remap hmmer

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• add user db targets; init write config

  bluegenes

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• Nuke the rest of dammit.tasks

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• Strip out more doit utils

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• add .vscode to gitignore

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• Add --version switch

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• Remove help from remap hmmer

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• enable print config

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Commits on Apr 25, 2020

• fix configfile printing

  bluegenes

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• get dammit databases subcommand working again

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• change cmd order

  bluegenes

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• fix configfiles

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Commits on Apr 26, 2020

• add shmlast to pipeline yml; fix targeting

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Commits on Apr 27, 2020

• enable busco

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• upd snkmk

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Commits on May 8, 2020

• refactor databases target gen

  camillescott

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• Bring in busco support

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• change busco wrapper to enable config

  bluegenes

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Commits on May 9, 2020

• comment out in progress rule

  bluegenes

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• Fix generate_annotation_targets, convert annotate to click parsing

  camillescott

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• merge in remove_argparse branch

  bluegenes

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• upd busco databases, fix busco targeting in run

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  f1a2fe6

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• fix busco db in run

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• working databases download

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• working busco run!

  bluegenes

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• move addl setup rule to new branch

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Commits on May 15, 2020

• Merge pull request #179 from dib-lab/add_busco_config

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• Merge pull request #177 from dib-lab/remove_argparse

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• Add in best-hits step and fix database attribute in gff3 outputs

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Commits on May 16, 2020

• seems to be working

  bluegenes

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Commits on May 29, 2020

• Fix file output naming conventions, start migrating config locations

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Commits on May 30, 2020

• fix paths in ini config

  bluegenes

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• Rewire temp folders and add config output subcommands

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• Merge in BUSCO config fixes

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• Add temp directory cleaning command

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• Merge pull request #185 from dib-lab/extricate_fileio

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• add busco plotting

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• Merge branch 'decompose' into plot_busco

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Commits on Jun 26, 2020

• message formatting

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• Merge pull request #186 from dib-lab/plot_busco

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Commits on Aug 7, 2020

• Add tests for wrappers and components (#188)

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• use mamba for conda installations (#193)

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Commits on Oct 26, 2020

• Nuke it from orbit: general clean-up and bugfixing (#196)

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Commits on Oct 30, 2020

• Refactor GFF3 conversion code to fix ID non-determinism with threading (#200)

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Commits on Jan 13, 2021

• Snakefile formatting and file hierarchy cleanup (#201)

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Commits on Jan 14, 2021

• Remove busci.ini download as part of databases pipeline.

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• --n-threads can be set by environment variable

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Commits on Jan 15, 2021

• Add nice output to run commands

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Commits on Jan 22, 2021

• Remove extraneous print

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• Add an environment variable DAMMIT_TESTING_TEMP_BASE_DIR to set a static location of conda environment during test sessions; tempdir_factory is used per-session if this variable is not defined

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• Merge pull request #204 from dib-lab/ui_improvements

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• Merge pull request #205 from dib-lab/conda_testing_configuration

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Commits on Jan 23, 2021

• Add dammit-transcriptome-stats to annotation workflow

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Commits on Jan 25, 2021

• Add transcriptome_stats task to all pipelines

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• add rich to environment requirements

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• Fix typo in pipelines definitions

  camillescott

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• Update shmlast version in requirements.txt; add environment name to environment.yml

  camillescott

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• add hmmscan and Pfam-A to quick pipeline (otherwise the gff3 conversion isn't performed)

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• environment suggestions

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• add missing dep on curl

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• Merge pull request #207 from luizirber/environment_suggestions

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Commits on Jan 28, 2021

• First pass: github actions for conda and pytest

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• Remove .travis.yml

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• add master and staging_v2 to triggers

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• Remove python 3.9 from test matrix (for now)

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• Don't set DAMMIT_DB_DIR

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• Remove macos from matrix (for now)

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• Add DAMMIT_DB_DIR back as global environment var

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• remove tilde from dammit_db_dir

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• Add lengths file output to test_components::TestTranscriptomeStats

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• Update annotate_user_database docstring with --n-threads

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• Update udb data for fixed quick pipeline definition

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• Merge branch 'actions_migration' into fix_quick_test_data

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• Merge pull request #210 from dib-lab/fix_quick_test_data

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• Add snakemake environment caching step

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• Implement database cache

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• Export DAMMIT_TESTING_TEMP_BASE_DIR

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• Remove unused annotate.py

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• Extricate original logging

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• Merge pull request #211 from dib-lab/snakemake_env_cache

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• Merge branch 'v2_staging' into cleanup

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• Remove import of deprecated logging

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• Merge pull request #212 from dib-lab/cleanup

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• Sketch out BUSCO to GFF3 conversion

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• Add attributes column to BUSCO_to_GFF3 converter and fix starting coordinate

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Commits on Jan 29, 2021

• Add BUSCO conversion to Snakemake workflow

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• Update test data with BUSCO hits

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• Remove unused pom.50.fa test data

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• Add larger pom subset as test data:

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• Handle case where there are no BUSCO hits

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• Test multiple busco groups

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• Merge pull request #213 from dib-lab/busco_gff_output

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• Attempt making paths portable

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• Use env context

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• Try using runner.temp for dammit data

  camillescott

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• dammit how does this work

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• Add support for Snakemake extra args to annotate and databases

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Commits on Jan 30, 2021

• Add test for extra snakemake args under annotate subcommand

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Commits on Feb 2, 2021

• Use quick pipeline for snakemake args test

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• Merge pull request #219 from dib-lab/extra_snakemake_args

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Commits on Feb 3, 2021

• Add --name-map option to dammit annotate-fasta to remap names back to originals

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• Add test data for dammit annotate-fasta --name-map

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• Use iloc instead of bracket indexing, as bracket indexing doesn't actually index positionally

  camillescott

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• Expose --rename/--no-rename in annotate CLI to enable mapping of renamed transcripts back to originals

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• Expose --split-regex in the dammit run annotate CLI with --regex-rename

  camillescott

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• Fix Infernal typo

  camillescott

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Commits on Feb 4, 2021

• Add a verbosity flag

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• BUSCO v5: add a BUSCOTableParser that properly splits out the coordinates; update busco-to-gff3 and converters for v5 format

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• Use set() to fix strange bug where multiple HMMER targets are generated when multi busco groups are used

  camillescott

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• Pass --global-evalue to BUSCO

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• Handle no BUSCO hits in table parser

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Commits on Feb 9, 2021

• Update test data and tests with data that works for BUSCO v5

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• Update busco wrapper test for smaller test data

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Commits on Feb 10, 2021

• py.test captures STDOUT and STDERR

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• Add proper --busco-group flag to test_annotate_dbdir

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• Merge branch 'v2_staging' into test_busco_v5

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• Merge pull request #223 from dib-lab/test_busco_v5

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• Merge pull request #222 from dib-lab/verbosity

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Commits on Feb 12, 2021

• Merge branch 'v2_staging' into expose_rename_regex

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• Update generate-test-data.sh with --regex-rename

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• Add --regex-rename test

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• Actually add regex-rename test-data

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• Merge pull request #221 from dib-lab/expose_rename_regex

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• verbose pandas output

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• Sort columns in compare_gff

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Commits on Mar 15, 2021

• Add a --fail-on-repeats flag to and set it true when user runs annotate pipelien with

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Commits on Mar 18, 2021

• Merge pull request #215 from dib-lab/actions_paths

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• Update no-rename test-data to use --quick pipeline

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Commits on May 26, 2021

• Merge pull request #226 from dib-lab/norename_tests

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