bokulich-lab RESCRIPt issues

bokulich-lab / RESCRIPt

REference Sequence annotation and CuRatIon Pipeline

BSD 3-Clause "New" or "Revised" License

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issues

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get-ncbi-genomes: custom rank information

#194 nbokulich opened 1 week ago
0
FIX: update `get-ncbi-genomes` to use genome accession IDs as taxonomy IDs

#193 misialq closed 1 week ago
3
MAINT: refactor GTDB taxonomy parser

#192 nbokulich closed 3 weeks ago
0
BUG: gtdb taxonomy parser

#191 nbokulich closed 3 weeks ago
1
Revert "DEP: q2-longitudinal"

#190 misialq closed 1 month ago
1
TEMPFIX: skip unit tests that rely on q2-longitudinal if it is not installed

#189 nbokulich closed 1 month ago
1
TST: fixing test failures from python 3.9 update

#188 lizgehret closed 1 month ago
1
CI: shotgun to amplicon

#187 lizgehret closed 1 month ago
0
CI: adds command to run tests

#186 lizgehret closed 1 month ago
1
get-ncbi-data Command Error

#185 rachelhawrit closed 1 month ago
1
ENH: Adds ability to fetch GTDB v220 to get-gtdb-data

#184 mikerobeson closed 1 month ago
0
ENH: Add the ability to fetch the latest GTDB database (v220) to `get-gtdb-data`

#183 mikerobeson closed 1 month ago
1
full SILVA LSU download

#182 sghignone closed 2 months ago
3
Add UNITE v10 DOIs

#181 colinbrislawn closed 2 months ago
0
which rescript version for qiime2 2022.11?

#180 PeSteff closed 3 months ago
2
Fix misplaced comma in bibtex

#179 ebolyen closed 4 months ago
0
DOC: fixes citation formatting reqs for sphinx docs builds

#178 lizgehret closed 4 months ago
1
LINT: fixing a couple of flake8 errors

#177 lizgehret closed 4 months ago
0
No more types genomics

#176 Oddant1 closed 4 months ago
3
providing primers for `trim-alignment` provides different output vs explicit column positions for the same primers.

#175 mikerobeson opened 5 months ago
0
ENH: adds `--p-n-threads` option to `trim-alignment`

#174 mikerobeson closed 1 month ago
1
ENH: `trim-alignment`, add `--p-addfragments` flag when using primer search option.

#173 mikerobeson closed 5 months ago
1
fixed README badges

#172 nbokulich closed 5 months ago
0
Rescript installation in q2-amplicon-2023.9

#171 ARW-UBT closed 5 months ago
1
Update of README.

#170 mikerobeson closed 5 months ago
17
get-gtdb refactor

#169 mikerobeson closed 5 months ago
0
ENH: Add option to download the corrected `214.1` GTDB database.

#168 mikerobeson closed 5 months ago
2
ENH: Add option to download `ssu_all_<release>.tar.gz` from GTDB.

#167 mikerobeson closed 5 months ago
1
patch get_unite

#166 colinbrislawn closed 7 months ago
0
Update help text for clarity: `dereplicate --p-mode super`

#165 mikerobeson opened 9 months ago
0
DEP: drop q2-longitudinal

#164 ebolyen closed 9 months ago
3
Remove heavy dependencies

#163 ebolyen opened 9 months ago
5
Update ci-dev.yaml

#162 ebolyen closed 9 months ago
5
CI: use qiime2/distributions for release cycle

#161 ebolyen closed 9 months ago
0
Authentication error with Option 2: Install within QIIME 2 environment

#160 singhdharmesh closed 1 month ago
1
orient-seqs: accept FASTQ data as input

#159 nbokulich opened 12 months ago
2
Sequence identifier warnings from `get-ncbi-data`.

#158 mikerobeson opened 1 year ago
0
get-gtdb-data: 214 release is new default

#157 nbokulich closed 1 year ago
0
Add support for gtdb release 214

#156 magicprotoss closed 1 year ago
1
ENH: get_rdp_data

#155 mikerobeson closed 11 months ago
2
ENH: initial draft of `get-gtdb`

#154 mikerobeson closed 1 year ago
10
ENH: enable genome fetching using NCBI Datasets

#153 misialq closed 1 year ago
6
How to train the classifier with mixed forward primers?

#152 BirongZhang closed 1 year ago
2
REVERT future warning for orient-seqs

#151 nbokulich closed 1 year ago
0
MAINT: Add future deprecation warning for orient-seqs

#150 mirand863 closed 1 year ago
4
MAINT: update `orient-seqs` to use vsearch `orient`

#149 mirand863 closed 1 year ago
4
MAINT: update copyright headers

#148 misialq closed 1 year ago
0
DEP: Fix joblib for ncbi.py

#147 mikerobeson closed 1 year ago
2
MAINT: update `orient-seqs` to use vsearch `orient`

#146 nbokulich closed 1 year ago
0
Use NCBI API keys in get-ncbi-data command

#145 hemprichbennett opened 1 year ago
0