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dib-lab
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genome-grist
map Illumina metagenomes to genomes!
https://dib-lab.github.io/genome-grist/
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use directsketch to download genomes
#315
ctb
opened
1 week ago
0
WIP: Use `sourmash_plugin_branchwater`
#314
ctb
closed
6 days ago
0
WIP: update genome-grist to modern days (Sep 2024)
#313
ctb
opened
2 months ago
1
modernize genome-grist :)
#312
ctb
opened
2 months ago
0
a passing thought on contaminated references
#311
clb21565
opened
3 months ago
0
Update pytest requirement from <7.5.0,>=5.1.2 to >=5.1.2,<8.1.0
#310
dependabot[bot]
opened
9 months ago
0
Bump actions/cache from 3 to 4
#309
dependabot[bot]
opened
10 months ago
0
Bump lxml from 4.9.3 to 5.1.0
#308
dependabot[bot]
opened
10 months ago
0
Bump lxml from 4.9.3 to 5.0.1
#307
dependabot[bot]
closed
10 months ago
1
Bump lxml from 4.9.3 to 5.0.0
#306
dependabot[bot]
closed
10 months ago
1
Bump pytest-dependency from 0.5.1 to 0.6.0
#305
dependabot[bot]
opened
10 months ago
0
Bump lxml from 4.9.3 to 4.9.4
#304
dependabot[bot]
closed
10 months ago
1
Bump actions/setup-python from 4 to 5
#303
dependabot[bot]
opened
11 months ago
0
Bump conda-incubator/setup-miniconda from 2 to 3
#302
dependabot[bot]
opened
12 months ago
0
Bumping bcftools to 1.18 in bcftools.yml?
#301
scunnac
opened
1 year ago
0
MRG: fix list in output doc
#300
ctb
closed
1 year ago
0
MRG: fix sketch command in configuring doc
#299
ctb
closed
1 year ago
0
Bump actions/checkout from 3 to 4
#298
dependabot[bot]
closed
1 year ago
0
revisit read naming - /1 and /2
#297
ctb
opened
1 year ago
0
update sourmash command in docs to include *gz on configuring page
#296
jessicalumian
closed
1 year ago
1
switch to using `get-some-ncbi-genomes`
#295
ctb
opened
1 year ago
0
raw read processing: `/1`, `/2` not always added/specified properly
#294
bluegenes
opened
1 year ago
0
fix documentation site to be better/nicer
#293
ctb
opened
1 year ago
0
Bump lxml from 4.9.2 to 4.9.3
#292
dependabot[bot]
closed
1 year ago
0
prioritize genomes found in previous samples when running genome grist
#291
clb21565
opened
1 year ago
2
Bump snakemake from 7.25.0 to 7.30.1
#290
dependabot[bot]
opened
1 year ago
1
Update pytest requirement from <7.4.0,>=5.1.2 to >=5.1.2,<7.5.0
#289
dependabot[bot]
closed
1 year ago
0
Bump snakemake from 7.25.0 to 7.29.0
#288
dependabot[bot]
closed
1 year ago
1
Bump snakemake from 7.25.0 to 7.28.3
#287
dependabot[bot]
closed
1 year ago
1
Bump snakemake from 7.25.0 to 7.28.2
#286
dependabot[bot]
closed
1 year ago
1
Bump snakemake from 7.25.0 to 7.28.1
#285
dependabot[bot]
closed
1 year ago
1
Insert a list of accessions into the `samples:` section of the `config.yml` file!
#284
ccbaumler
opened
1 year ago
1
Using `--cluster` parameter to run jobs
#283
ccbaumler
opened
1 year ago
1
Bump snakemake from 7.25.0 to 7.26.0
#282
dependabot[bot]
closed
1 year ago
1
Bump snakemake from 7.25.0 to 7.25.4
#281
dependabot[bot]
closed
1 year ago
1
Bump snakemake from 7.25.0 to 7.25.3
#280
dependabot[bot]
closed
1 year ago
1
Bump snakemake from 7.25.0 to 7.25.2
#279
dependabot[bot]
closed
1 year ago
1
Problem with grist output
#278
marsfro
opened
1 year ago
0
add check to ignore genome(s) that cannot be up downloaded
#277
bcpd
opened
1 year ago
4
Update pytest requirement from <7.3.0,>=5.1.2 to >=5.1.2,<7.4.0
#276
dependabot[bot]
closed
1 year ago
1
Update pandas, pytest, and sourmash requirements.
#275
dependabot[bot]
closed
1 year ago
0
Bump snakemake from 7.24.2 to 7.25.0
#274
dependabot[bot]
closed
1 year ago
0
Problem installing geome-grist & spacegraphcats
#273
hehouts
opened
1 year ago
2
Bump snakemake from 7.24.0 to 7.24.2
#272
dependabot[bot]
closed
1 year ago
0
Bump snakemake from 7.24.0 to 7.24.1
#271
dependabot[bot]
closed
1 year ago
1
MRG: Ignore DeprecationWarning from sourmash in tests.
#270
ctb
closed
1 year ago
0
Bump snakemake from 7.20.0 to 7.24.0
#269
dependabot[bot]
closed
1 year ago
2
Problem with rule extract_leftover_reads_wc (DeprecationWarning: Implementing implicit namespace packages)
#268
jessicalumian
opened
1 year ago
1
Bump snakemake from 7.20.0 to 7.22.0
#267
dependabot[bot]
closed
1 year ago
1
maximum number of gather hashes on report graph and finding numbers of hashes that don't match anything
#266
jessicalumian
opened
1 year ago
2
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