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Staging for version 2.0 #206

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@camillescott camillescott commented Jan 25, 2021

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camillescott and others added 30 commits November 6, 2019 19:37
@camillescott
add rename and stats components
e887d2a
@camillescott
add remap hmmer component
0b4ce27
@camillescott
remove converted tasks
daf61bf
@camillescott
move busco parsers to fileio submodule
f28101e
@camillescott
convert and filter components
4e0207a
@camillescott
Add conversion components
fcf9d04
@camillescott
Get gff3 merge command working
a37d5dd
@bluegenes
add busco, transdecoder wrappers
6293805
@camillescott
ADd annotate component
b562c25
@camillescott
Merge branch 'decompose' of github.com:camillescott/dammit into decom…
06fd042 
…pose
@camillescott
add rename-transcriptome wrapper
bb4b203
@bluegenes
add transdecoder test data, rules
56ce4b7
@bluegenes
add busco rule, busco testdata
8a595bb
@bluegenes
add last
6165178
@bluegenes
add infernal wrapper and rule
d4f7bf1
@camillescott
First round of workflow structuring: database download
cdaf6ec
@camillescott
merge download rules
accacaf
@bluegenes
add transdecoder, last, infernal, hmmer wrappers
9f719eb
@bluegenes
init hmmer, transdecoder workflows
388ce3e
@camillescott
code removal
86c25c3
@camillescott
Merge branch 'decompose' of github.com:camillescott/dammit into decom…
0edabeb 
…pose
@bluegenes
add yaml; init annot snakes
fd22338
@bluegenes
init config changes; init main snake
06b5ab6
@bluegenes
yml db file
aa11da7
@camillescott
Merge branch 'decompose' of github.com:camillescott/dammit into decom…
2778bea 
…pose
@bluegenes
working snakemake calls
e111db1
@bluegenes
fix md5 downloads
2429aaf
@bluegenes
ignore metalink for now
654d4a8
@bluegenes
fix lastdb wrapper
faa5671
@bluegenes
working transdecoder
a5564b8
@camillescott
Merge pull request #219 from dib-lab/extra_snakemake_args
22bfbb4
@camillescott
Add --name-map option to dammit annotate-fasta to remap names back to…
41b95f3 
… originals
@camillescott
Add test data for dammit annotate-fasta --name-map
7766172
@camillescott
Use iloc instead of bracket indexing, as bracket indexing doesn't act…
2073274 
…ually index positionally
@camillescott
Expose --rename/--no-rename in annotate CLI to enable mapping of rena…
06ff3bd 
…med transcripts back to originals
@camillescott
Expose --split-regex in the dammit run annotate CLI with --regex-rename
2fc126d
@camillescott
Fix Infernal typo
5f4a869
@camillescott
Add a verbosity flag
d35515a
@camillescott
BUSCO v5: add a BUSCOTableParser that properly splits out the coordin…
56f7076 
…ates; update busco-to-gff3 and converters for v5 format
@camillescott
Use set() to fix strange bug where multiple HMMER targets are generat…
9bdd7b9 
…ed when multi busco groups are used
@camillescott
Pass --global-evalue to BUSCO
221a1df
@camillescott
Handle no BUSCO hits in table parser
f0ea818
@camillescott
Update test data and tests with data that works for BUSCO v5
f907867
@camillescott
Update busco wrapper test for smaller test data
2bac59a
@camillescott
py.test captures STDOUT and STDERR
cd8df6d
@camillescott
Add proper --busco-group flag to test_annotate_dbdir
77b5eee
@camillescott
Merge branch 'v2_staging' into test_busco_v5
7ce1650
@camillescott
Merge pull request #223 from dib-lab/test_busco_v5
27706a9
@camillescott
Merge pull request #222 from dib-lab/verbosity
faa4ad5 
Add a verbosity flag
@camillescott
Merge branch 'v2_staging' into expose_rename_regex
b038df3
@camillescott
Update generate-test-data.sh with --regex-rename
bc82940
@camillescott
Add --regex-rename test
627db02
@camillescott
Actually add regex-rename test-data
470ca6d
@camillescott
Merge pull request #221 from dib-lab/expose_rename_regex
13e9d95
@camillescott
verbose pandas output
fa3410c
@camillescott
Sort columns in compare_gff
d4c4636
@camillescott
Add a --fail-on-repeats flag to and set it true when user runs annota…
e2159aa 
…te pipelien with
@camillescott
Merge pull request #215 from dib-lab/actions_paths
4124c0d
@camillescott
Update no-rename test-data to use --quick pipeline
d605b70
@camillescott
Merge pull request #226 from dib-lab/norename_tests
e51584d
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4 participants

@camillescott @bluegenes @luizirber