bokulich-lab q2-assembly issues

bokulich-lab / q2-assembly

QIIME 2 plugin for (meta)genome assembly.

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

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issues

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ENH: updates spades to 4.0.0

#102 misialq opened 1 week ago
0
ENH: add parallelization support to evaluate-spades action

#101 misialq opened 1 week ago
0
MAINT: use tempfiles in tests

#100 misialq closed 1 month ago
1
ENH: add action to collate genomes to GenomeData[DNASequences]

#99 DorielaGrabocka closed 1 month ago
1
BUG: 'meta' preset is allowed by q2-assembly command assemble megahit despite 'meta' not being a preset option for megahit

#98 schaermi opened 2 months ago
0
ENH: add action to combine FeatureData[Sequence] artifacts into one GenomeData[DNASequence] artifact

#97 misialq closed 1 month ago
0
ENH: QUAST outputs downloaded genome artifacts

#96 DorielaGrabocka closed 1 month ago
3
REF: fix private imports for q2-types refactor

#95 ebolyen closed 2 months ago
4
Use new test config

#94 Oddant1 closed 3 months ago
2
ENH: output fetched reference genomes from 'evaluate-quast'

#93 misialq closed 1 month ago
0
ENH: add 'filter-contigs' action

#92 misialq opened 4 months ago
0
FIX: pass BAM files to metaquast in the correct order

#90 misialq closed 2 months ago
3
ENH: filter contigs by length

#91 rhernandvel opened 4 months ago
0
ENH: action to rename contigs using shortuuid, uuid3, uuid4 or uuid5

#89 DorielaGrabocka closed 4 months ago
4
ENH: make contig IDs unique across samples

#88 DorielaGrabocka closed 4 months ago
1
DEV: 2024.10

#87 nbokulich closed 5 months ago
0
PIN: adds pysam back into recipe file

#86 lizgehret closed 5 months ago
0
ENH: evaluate-contigs action outputs a results table to enable filtering of samples

#85 DorielaGrabocka closed 4 months ago
1
ENH: add an action to filter `SampleData[Contigs]`

#84 misialq opened 6 months ago
1
ENH: add action to rename contigs

#83 misialq closed 4 months ago
0
ENH: make contig IDs unique across all samples

#82 misialq closed 4 months ago
0
ENH: add more indexing and read mapping options

#81 misialq closed 4 months ago
6
LANG: dependency testing for python 3.9 updates to metagenome distro

#80 lizgehret closed 5 months ago
8
CI: update the distro

#79 misialq closed 7 months ago
0
ENH: allow passing already aligned reads to `evaluate-quast`

#78 DorielaGrabocka closed 6 months ago
1
ENH: evaluate-contigs action should output a results table to enable filtering of samples

#77 misialq closed 4 months ago
0
BUG: download buttons in the QUAST viz are broken

#76 misialq closed 6 months ago
1
FIX: QUAST visualization button links should point to the correct set of files

#75 misialq closed 6 months ago
1
ENH: add the ability to generate QUAST visualizations without Icarus viewers

#74 misialq closed 6 months ago
1
ENH: allow contig QC evaluation without drawing the Icarus plots

#73 misialq closed 6 months ago
0
BUG: action `assemble-megahit` does not allow for `--p-num-cpu-threads > 1`

#72 Sann5 closed 7 months ago
3
No more types genomics

#71 Oddant1 closed 9 months ago
4
ENH: update `insilicoseq` to 1.6.0

#70 misialq closed 4 months ago
2
ENH: allow passing already aligned reads to `evaluate-quast`

#69 misialq closed 6 months ago
0
ENH: co-assembling contigs from multiple samples (#22)

#68 DorielaGrabocka closed 7 months ago
1
DEP: add pysam to the list of dependencies

#67 misialq closed 11 months ago
1
BUG: `MultiMAGSequencesDirFmt` does not have a manifest in `index_mags`

#66 colinvwood opened 11 months ago
0
adding more params to `evaluate_contigs`

#65 mikerobeson closed 1 year ago
2
BUG: Download buttons for the `assembly evaluate-contigs` visualization not producing PDFs, etc..

#64 mikerobeson closed 1 year ago
2
error informatively on empty input files for `index-contigs`

#63 colinvwood closed 1 year ago
4
Update help text for `assemble-spades --p-threads --p-memory`

#62 mikerobeson opened 1 year ago
0
MAINT: update README badges

#61 misialq closed 1 year ago
0
BUG: action `generate-reads` is missing the `pysam` dependency

#60 misialq closed 11 months ago
3
collect all contig files inside index-contigs

#59 colinvwood closed 1 year ago
1
BUG: index-contigs collects only .fa files

#58 colinvwood closed 1 year ago
0
BUG: fix phred-offset autodetection

#57 misialq closed 1 year ago
3
BUG: `assembly assemble-spades` auto-detection of phred-offset error

#56 mikerobeson closed 1 year ago
0
update help text for `assemble-spades --p-meta`

#55 mikerobeson closed 1 year ago
3
Issue 42: expose additional visualizations generated by QUAST in the evaluate-contigs visualization

#54 Sann5 closed 1 year ago
2
CI: update to new CI

#53 ebolyen closed 1 year ago
2