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Issues list

Add nf-core style testing suite for the Nextflow side of the code testing
#389 opened Nov 8, 2024 by madeline-scyphers v2.0.0-beta7
Add logging in python side of DRAM documentation Improvements or additions to documentation
#388 opened Nov 8, 2024 by madeline-scyphers v2.0.0-beta6
Question about DRAM-v output
#386 opened Nov 5, 2024 by deminatanja
Add much better logging throughout the pipeline documentation Improvements or additions to documentation
#382 opened Oct 21, 2024 by madeline-scyphers v2.0.0-beta7
Add better input validation for input combinations that don't make sense documentation Improvements or additions to documentation package Package structure
#381 opened Oct 21, 2024 by madeline-scyphers v2.0.0-beta7
Create a DOI for the DRAM software with zenodo package Package structure
#380 opened Oct 17, 2024 by madeline-scyphers v2
When writing outputs or logs, if already exists, append with something enhancement New feature or request
#378 opened Oct 17, 2024 by madeline-scyphers v2
All CLI help text defaults should pull from the config default, the config defualt instead of being hard coded CLI Command line interface stuff documentation Improvements or additions to documentation
#377 opened Oct 17, 2024 by madeline-scyphers v2
Add close inactive issue workflow/action CI/CD Related to CI/CD
#376 opened Oct 17, 2024 by madeline-scyphers
1 task
Future
DRAM visualization (product) tracking issue package Package structure
#374 opened Oct 17, 2024 by madeline-scyphers Future
DRAM v2 README has too much hard coded things in it (like the --help output) documentation Improvements or additions to documentation
#373 opened Oct 17, 2024 by madeline-scyphers v2
DRAM trees and adjectives implementation enhancement New feature or request process Related to DRAM process
#372 opened Oct 17, 2024 by madeline-scyphers Future
Better user Nextflow Configuration override configuration Things to do with DRAM or Nextflow configuration
#371 opened Oct 17, 2024 by madeline-scyphers v2.0.0-beta7
Update environment.yml package Package structure refactor Refactoring without or minimal functional changes
#370 opened Oct 17, 2024 by madeline-scyphers v2
Integrate whatever we feel is useful from the nf-core template CI/CD Related to CI/CD package Package structure testing
#369 opened Oct 17, 2024 by madeline-scyphers v2
1
Add back DRAM v1 testing suite for v2 CI/CD Related to CI/CD testing
#368 opened Oct 17, 2024 by madeline-scyphers v2.0.0-beta6
Update docs from Wiki for DRAM v2, probably move to readthedocs documentation Improvements or additions to documentation
#367 opened Oct 17, 2024 by madeline-scyphers v2.0.0-beta6
Decouple DRAM v2 tool code from Nextflow code package Package structure
#366 opened Oct 17, 2024 by madeline-scyphers v2.0.0-beta6
Dram-v on Virsorter2 output: pandas error, unexpected EOF, syntax error
#363 opened Oct 11, 2024 by deminatanja
1
ListUtil.c: loadable library and perl binaries are mismatched
#362 opened Oct 6, 2024 by 473021677
State of DRAM2 Usage Question
#361 opened Sep 25, 2024 by donovan-parks v2
1
DRAM-setup.py in v1.5.0 has invalid syntax
#360 opened Sep 25, 2024 by donovan-parks
ValueError: Format is not VIRSorter2, and can't find VIRSorter endings on fasta header
#359 opened Sep 20, 2024 by liaohu1231
4
Controlling CPU usage for the DRAM.py distill pipeline for DRAM v.1.5.0 Usage Question
#358 opened Aug 19, 2024 by nataliesarno
1
Pathway abundances?
#357 opened Aug 8, 2024 by Manso002
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