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105 Open 67 Closed
105 Open 67 Closed
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Issues list

use directsketch to download genomes
#315 opened Nov 13, 2024 by ctb
modernize genome-grist :)
#312 opened Sep 18, 2024 by ctb
4 tasks
a passing thought on contaminated references
#311 opened Jul 29, 2024 by clb21565
Bumping bcftools to 1.18 in bcftools.yml?
#301 opened Oct 18, 2023 by scunnac
revisit read naming - /1 and /2
#297 opened Aug 27, 2023 by ctb
switch to using get-some-ncbi-genomes
#295 opened Jul 31, 2023 by ctb
raw read processing: /1, /2 not always added/specified properly
#294 opened Jul 12, 2023 by bluegenes
fix documentation site to be better/nicer
#293 opened Jul 8, 2023 by ctb
prioritize genomes found in previous samples when running genome grist
#291 opened Jun 29, 2023 by clb21565
2
Insert a list of accessions into the samples: section of the config.yml file! code documentation Improvements or additions to documentation
#284 opened Jun 10, 2023 by ccbaumler
1
Using --cluster parameter to run jobs documentation Improvements or additions to documentation enhancement New feature or request good first issue Good for newcomers
#283 opened Jun 10, 2023 by ccbaumler
1
Problem with grist output
#278 opened Apr 19, 2023 by marsfro
add check to ignore genome(s) that cannot be up downloaded
#277 opened Apr 16, 2023 by bcpd
4
Problem installing geome-grist & spacegraphcats
#273 opened Mar 22, 2023 by hehouts
2
Problem with rule extract_leftover_reads_wc (DeprecationWarning: Implementing implicit namespace packages)
#268 opened Feb 16, 2023 by jessicalumian
1
maximum number of gather hashes on report graph and finding numbers of hashes that don't match anything
#266 opened Feb 7, 2023 by jessicalumian
2
What should we benchmark?
#263 opened Dec 20, 2022 by ccbaumler
1
use picklists for ignoring identifiers instead of custom coding it in the Snakefile
#262 opened Dec 18, 2022 by ctb
Errors if genome-grist run on Marine metagenomes
#241 opened Nov 27, 2022 by jeanzzhao
25
filesystem latency error
#240 opened Nov 14, 2022 by jeanzzhao
8
print out important snakemake args when invoking genome-grist --help
#239 opened Nov 3, 2022 by clb21565
1
add printout of version information when running genome-grist
#236 opened Oct 20, 2022 by ctb
would it be helpful to add ln to configuration instructions?
#235 opened Oct 19, 2022 by jessicalumian
draft release protocol for genome-grist
#234 opened Sep 30, 2022 by ctb
explore myst-nb for notebooks
#231 opened Sep 28, 2022 by ctb
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