bokulich-lab q2-moshpit issues

bokulich-lab / q2-moshpit

MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking

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

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issues

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CI: fix mamba version and some test file paths

#208 misialq closed 1 day ago
4
BUG: ParseError when running `eggnog-hmmer-search`

#207 DorielaGrabocka opened 1 week ago
0
Does not return Collection and List will no longer be allowed

#206 Oddant1 closed 2 weeks ago
2
BUG: collate_kraken2_outputs returns list

#205 Oddant1 closed 2 weeks ago
0
LANG: relax busco pin for python 3.10 update

#204 lizgehret closed 2 weeks ago
3
ENH: Wrap fastp in moshpit

#203 rhernandvel opened 3 weeks ago
1
ENH: Adds SampleData[JoinedSequencesWithQuality] as input for classify-Kraken2

#202 cherman2 opened 3 weeks ago
2
FIX: update how fetch-kaiju-db action discovers DB URLs

#201 misialq closed 1 month ago
1
ENH: parallelize Kaiju classification

#200 misialq closed 1 day ago
2
ENH: parallelize classification with Kaiju

#199 misialq closed 1 day ago
1
ENH: add action to build a Kaiju database

#198 misialq opened 1 month ago
1
BUG: `fetch-kaiju-db` action does not work after Kaiju server shutdown

#197 misialq closed 1 month ago
0
ENH: add action to generate human pangenome index and filter against it

#196 misialq closed 1 month ago
1
CI: bring back QIIME CI

#195 misialq closed 2 months ago
0
REF: remove private imports for q2-types refactor

#194 ebolyen closed 1 month ago
4
use new test config

#193 Oddant1 closed 2 months ago
2
MAINT: Ortholog types updates to pair with q2-types PR#338

#192 lizgehret closed 2 months ago
3
FIX: Kraken2/Bracken feature tables/taxonomies should contain unclassified counts

#191 misialq closed 1 month ago
2
LANG: more pkgdata updates

#190 lizgehret closed 2 months ago
5
LANG: updating pkg data dirs to fix metagenome prepare failures

#188 lizgehret closed 2 months ago
6
PREP: updating pkg data dirs to fix metagenome prepare failures

#187 lizgehret closed 3 months ago
2
ENH: import MAGs while tracking original names from the fasta files

#186 rhernandvel opened 3 months ago
0
MAINT: make PR template available

#185 Sann5 closed 1 month ago
1
ENH: add eggnog-hmmer-search action

#184 Sann5 closed 3 months ago
1
FIX: correctly label 'Unclassfied' MAGs in the respective taxonomy

#183 misialq closed 3 months ago
2
MAINT: update Python version in test CI

#182 misialq closed 3 months ago
2
TEST: include missing busco test files

#181 Sann5 closed 3 months ago
8
ENH: add action to transfer EggNOG annotations from annotated MAGs to the dereplicated MAGs

#180 misialq opened 3 months ago
0
BUG: unclassified MAGs result in empty taxonomic annotations with kraken2-to-mag-features in QIIME 2 2024.5

#179 pmomocabr closed 3 months ago
0
ENH: add action to extract a specific annotation into a feature table

#178 misialq closed 1 month ago
1
ENH: add action to estimate MAG abundance

#177 misialq closed 1 month ago
4
DEV: 2024.10

#176 nbokulich closed 4 months ago
0
MAINT: move partitioning and collating actions to q2-types

#175 VinzentRisch closed 2 weeks ago
11
BUG: add mags-derep test dir to package_data

#174 lizgehret closed 4 months ago
2
ENH: add `fetch-eggnog-hmmer-db` action

#173 Sann5 closed 3 months ago
3
MAINT: move partitioning and collating actions to q2-types

#172 misialq opened 4 months ago
0
CI: add new workflows

#171 misialq closed 4 months ago
3
CI: clean up dependencies

#170 misialq closed 4 months ago
0
ENH: add actions to filter MAGs

#169 misialq closed 4 months ago
5
ENH: add ortholog prediction with a HMMER through `search-eggnog-hmmer` action

#168 Sann5 closed 3 months ago
0
ENH: add `fetch-hmmer-db` action

#167 Sann5 closed 3 months ago
0
ENH: add action to filter `SampleData[MAGs]`

#166 misialq closed 4 months ago
1
ENH: add action to filter `FeatureData[MAG]`

#165 misialq closed 4 months ago
1
ENH: add action to get feature lengths

#164 misialq closed 4 months ago
1
ENH: add action to extract MAG lengths

#163 misialq closed 4 months ago
0
ENH: add action `fetch-busco-db` and modify `evaluate-busco` accordingly

#162 Sann5 closed 3 months ago
23
ENH: allow using BUSCOResult during MAG dereplication

#161 misialq opened 4 months ago
0
ENH: add an action to filter `SampleData[MAGs]` and `FeatureData[MAG]`

#160 misialq closed 4 months ago
0
ENH: allow `FeatureData[MAG]` as input to `evaluate_busco` action

#159 Sann5 closed 4 months ago
3
CI: bump codecov-action version to v4

#158 Sann5 closed 5 months ago
2