dib-lab charcoal issues

dib-lab / charcoal

Remove contaminated contigs from genomes using k-mers and taxonomies.

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WIP: update CI.

#240 ctb opened 11 months ago
0
MRG: update sourmash and snakemake dependencies

#239 ctb opened 11 months ago
0
Does charcoal not support installation via mamba?

#238 SchwarzEM opened 11 months ago
16
Both DEMO datasets Fails with: ImportError: cannot import name 'LineagePair' from 'sourmash.lca'

#237 JoshuaTCooper opened 1 year ago
1
Error in rule combine_postprocessing_csv

#236 sabdelrazek opened 1 year ago
0
GenBank genomes not found

#235 tgurbich opened 1 year ago
2
IndexError

#234 sabdelrazek closed 1 year ago
0
demo fails with "Error in snakemake invocation: Command '['snakemake', '-s', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/Snakefile', '--use-conda', '-j', '1', '-j', '4', '--configfile', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/conf/defaults.conf', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/conf/system.conf', 'demo/demo.conf']' returned non-zero exit status 1."

#233 JoshuaTCooper opened 1 year ago
0
What should we benchmark?

#232 ccbaumler opened 1 year ago
3
paper: Contamination detection and microbiome exploration with GRIMER

#231 ctb opened 1 year ago
0
explore unicity distance of individual contigs in database

#230 ctb opened 1 year ago
0
charcoal analysis of single assembly file

#229 gaworj opened 1 year ago
3
update database download to farm links

#228 ctb opened 2 years ago
0
add test requirements to ...environment? pip install? something?

#227 ctb opened 2 years ago
1
update `env-reporting.yml` version pins

#226 ctb opened 2 years ago
3
[MRG] fix `LCA_Database.gather(...)` call to use `LCA_Database.best_containment(...)`

#225 ctb closed 2 years ago
5
Demo failed with error message Error in rule make_contigs_search_taxonomy_wc, Error in rule compare_taxonomy_single_wc, Error in rule make_contigs_search_taxonomy_wc

#224 anilbaniya123 closed 2 years ago
8
[MRG] add matplotlib to report env

#223 taylorreiter closed 2 years ago
0
demo fails with "Error occurred while starting new kernel client for kernel 0287ef32-45b2-4f5d-8470-97ab4a40626a: Kernel didn't respond in 60 seconds"

#222 taylorreiter opened 2 years ago
5
add a disclaimer to the quickstart that it will take longer than 2min if the envs need to be created (e.g. first time running)?

#221 taylorreiter opened 2 years ago
0
change quick start installation to mamba?

#220 taylorreiter opened 2 years ago
0
Add tests for system conf `scaled` and `gather_scaled` values to match the default database scaled?

#219 taylorreiter opened 2 years ago
0
[MRG] update scaled back to 1000 to match rs207 scaled

#218 taylorreiter closed 2 years ago
0
updating default scaled to 2000 caused new value error

#217 taylorreiter closed 2 years ago
3
add developer docs

#216 taylorreiter opened 2 years ago
0
[MRG] update default db to rs207 reps

#215 taylorreiter closed 2 years ago
6
allow gzipped lineage files

#214 taylorreiter opened 2 years ago
0
DEMO FAILED

#213 giriarteS opened 2 years ago
0
update dbs to rs207

#212 taylorreiter closed 2 years ago
1
config parameterization of GATHER_MIN_MATCHES

#211 taylorreiter opened 2 years ago
0
I think `provided_lineages_file` is no longer optional

#210 taylorreiter opened 2 years ago
0
R parsers for stage1 and stage2 json files

#209 taylorreiter opened 2 years ago
1
organization of report directory

#208 taylorreiter opened 2 years ago
0
confused about some text in output of stage2 `stage2/*postprocess.txt`

#207 taylorreiter opened 2 years ago
0
output `stage1_genome_summary.csv` during target clean

#206 taylorreiter opened 2 years ago
3
look into plotsr for plotting relationships b/t genomes!

#205 ctb opened 2 years ago
0
update charcoal with functions from `sourmash.tax`

#204 ctb opened 2 years ago
0
[MRG] replace some of the utils functions with sourmash lca_utils

#203 ctb closed 2 years ago
1
[MRG] Switch to using picklists for storing matches, as opposed to saving a copy of the signatures.

#202 ctb closed 2 years ago
2
implement picklists!

#201 ctb closed 2 years ago
1
[WIP] update snakemake version

#200 ctb opened 2 years ago
0
running charcoal on GTDB: using snakemake to run really large charcoal runs

#199 taylorreiter opened 2 years ago
4
paper: ProDeGe: a computational protocol for fully automated decontamination of genomes

#198 taylorreiter opened 3 years ago
0
How do I decontaminate not only prokaryotes, but unicellular eukaryotes?

#197 SchwarzEM opened 3 years ago
7
paper: Removing contaminants from databases of draft genomes

#196 ctb opened 3 years ago
0
we should probably add some tests for the command line

#195 taylorreiter opened 3 years ago
0
[MRG] add `--help` option to click `run`

#194 bluegenes closed 3 years ago
0
charcoal targets won't start running with latest version of charcoal v0.1.dev327+gde4bd52

#193 taylorreiter closed 3 years ago
0
No cleaning with exact matches even when lineage is provided

#192 taylorreiter opened 3 years ago
5
[MRG] upgrade the command-line interface a bit

#191 ctb closed 3 years ago
0