cmkobel CompareM2 issues

cmkobel / CompareM2

🦠📇 Microbial genomes-to-report pipeline

https://CompareM2.readthedocs.io

GNU General Public License v3.0

52 stars 3 forks source link

issues

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Insatlling comparem2

#111 bharat1912 closed 1 day ago
2
installation issue

#110 flefler closed 2 months ago
6
Error in passthrough argument feature: `Invalid config definition: Config entry must start with a valid identifier.`

#109 cmkobel opened 2 months ago
4
Eggnog fails if version installed is above or equal to 2.1.7

#108 michoug closed 2 months ago
2
URL to manually download the databases?

#107 ruizhao087 closed 1 month ago
2
both bakta and prokka are run despite specify an annotator

#106 michoug closed 2 months ago
2
Update README.md

#102 wwood closed 2 months ago
0
Can't add more than a single string (file or glob) to the input_genomes parameter.

#101 cmkobel closed 4 months ago
2
Upgrade to snakemake 8

#100 cmkobel opened 4 months ago
1
Add ring and bi-plot for quality

#99 wala-github opened 5 months ago
0
--help

#98 cmkobel closed 4 months ago
2
Returns exit code 0 on error.

#97 cmkobel closed 4 months ago
2
Benchmarking

#96 cmkobel closed 4 months ago
0
Follow the standard file hierarchy for a snakemake pipeline.

#95 cmkobel closed 5 months ago
3
Remove mamba as dependency from bioconda recipe?

#94 cmkobel closed 4 months ago
1
Migrate to codeberg

#93 cmkobel closed 5 months ago
2
hat?

#92 cmkobel closed 6 months ago
0
Option to add .faa files for analysis downstream of gene calling

#91 cmkobel opened 7 months ago
0
Implement downloading ko00001.json

#90 cmkobel closed 6 months ago
2
Roary policy

#89 cmkobel closed 6 months ago
1
Naming of output directory.

#88 cmkobel closed 4 months ago
4
wget should not use --continue, but somehow otherwise never write to an alternatively named file.

#87 cmkobel opened 8 months ago
0
gtdbtk: mash: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory

#86 cmkobel closed 4 months ago
1
N<4, iqtree: ERROR: It makes no sense to perform bootstrap with less than 4 sequences.

#85 cmkobel closed 4 months ago
1
Remove busco?

#83 cmkobel closed 3 months ago
0
Prune test datasets

#82 cmkobel closed 3 months ago
0
mamba requirement is unnecessarily specific

#81 cmkobel closed 3 months ago
1
rule gtdb_download: curl: (77) error setting certificate file: /etc/ssl/certs/ca-bundle.crt

#79 cmkobel closed 8 months ago
1
Use newer uniref 100 database for kegg calling

#78 cmkobel closed 4 months ago
5
-v and --version unexpected incongruency

#77 cmkobel closed 8 months ago
1
Messy directories

#76 cmkobel opened 8 months ago
1
Portable disk image

#75 cmkobel closed 8 months ago
1
! dev.control() called without an open graphics device

#74 cmkobel closed 6 months ago
7
Syntenic core genome

#71 cmkobel closed 3 months ago
0
Midpoint rooting in the report tree?

#70 cmkobel opened 11 months ago
0
Interactive plots in the report document

#69 cmkobel opened 11 months ago
0
Alternative genome annotation

#68 cmkobel closed 4 months ago
2
Download databases without a dummy file being present

#67 cmkobel closed 3 months ago
3
Bioconda recipe simplification

#66 cmkobel closed 3 months ago
0
Reuse checkm2s output in kegg_pathway

#65 cmkobel closed 8 months ago
3
(roary) Could not solve for environment space

#64 cmkobel closed 11 months ago
2
Present snakefile in header

#63 cmkobel closed 11 months ago
1
Feature request

#62 magnusarntzen opened 11 months ago
3
Beer bug bounty 🍻🪲🐛

#61 cmkobel closed 3 months ago
1
Dry run fails when apptainer-compatible docker image is not already downloaded.

#60 cmkobel closed 11 months ago
3
User should be actively warned when not using apptainer.

#59 cmkobel closed 3 months ago
1
--configure input_files="genome.fna"

#58 cmkobel closed 8 months ago
1
Rename assemblycomparator2?

#57 cmkobel closed 3 months ago
2
Files inaccessible inside apptainer environment when working in a symlinked directory

#56 cmkobel closed 8 months ago
5
copied input files should be named *.fna, not *.fa

#55 cmkobel closed 3 months ago
0