Issues · Laura Denies / PathoFact · GitLab

spring-clean: VirSorter 4 of 4 tasks completed

#21 · created Apr 20, 2020 by Valentina Galata spring-clean clean-up dependencies
- CLOSED
- 1
- 1
updated Apr 21, 2020
spring-clean: HMMER 3 of 3 tasks completed

#22 · created Apr 20, 2020 by Valentina Galata spring-clean clean-up dependencies
- CLOSED
- 1
- 3
updated Apr 21, 2020
spring-clean: clean up YAML files

#23 · created Apr 20, 2020 by Valentina Galata spring-clean clean-up
- CLOSED
- 1
- 0
updated Apr 21, 2020
spring-clean: add workflow parameter 2 of 2 tasks completed

#24 · created Apr 20, 2020 by Valentina Galata spring-clean clean-up enhancement
- CLOSED
- 1
- 2
updated Apr 21, 2020
spring-clean: rm `configfile` from snakemake rule files

#25 · created Apr 20, 2020 by Valentina Galata spring-clean clean-up enhancement
- CLOSED
- 1
- 0
updated Apr 21, 2020
spring-clean: snakemake rules indentation

#26 · created Apr 20, 2020 by Valentina Galata spring-clean clean-up
- CLOSED
- 1
- 2
updated Apr 21, 2020
Snakemake rule messages

#27 · created Apr 20, 2020 by Valentina Galata Paper review - Microbiome - 1 enhancement
- CLOSED
- 1
- 2
updated Aug 06, 2020
spring-clean: logging

#28 · created Apr 20, 2020 by Valentina Galata spring-clean clean-up enhancement
- CLOSED
- 0
updated Apr 21, 2020
spring-clean: snakemake rules: use names in shell/run/script

#29 · created Apr 21, 2020 by Valentina Galata spring-clean clean-up
- CLOSED
- 0
updated Apr 30, 2020
spring-clean: test data set 3 of 3 tasks completed

#30 · created Apr 23, 2020 by Valentina Galata spring-clean clean-up enhancement
- CLOSED
- 1
updated Apr 29, 2020
spring-clean: args in virulence_prediction.py and rule classifier in the vir step

#31 · created Apr 23, 2020 by Valentina Galata spring-clean bug clean-up
- CLOSED
- 1
updated Apr 23, 2020
spring-clean: escape special chars in rules properly

#32 · created Apr 23, 2020 by Valentina Galata spring-clean clean-up enhancement
- CLOSED
- 0
updated Apr 30, 2020
spring-clean: add test workflow 3 of 3 tasks completed

#33 · created Apr 24, 2020 by Valentina Galata spring-clean clean-up enhancement
- CLOSED
- 0
updated Apr 30, 2020
Replace SignalP

#34 · created May 05, 2020 by Valentina Galata Paper review - Microbiome - 1 dependencies enhancement
- CLOSED
- 4
updated Sep 30, 2021
Update SignalP

#35 · created May 05, 2020 by Valentina Galata Paper review - Microbiome - 1 enhancement
- CLOSED
- 0
updated Jun 22, 2020
README.md update 3 of 3 tasks completed

#36 · created May 05, 2020 by Valentina Galata Paper review - Microbiome - 1 documentation
- CLOSED
- 1
updated Jan 12, 2021
PlasFlow threshold from config

#37 · created May 15, 2020 by Valentina Galata Paper review - Microbiome - 1 enhancement
- CLOSED
- 1
updated Jan 12, 2021
size_fasta is not used by seqkit

#38 · created May 15, 2020 by Valentina Galata Paper review - Microbiome - 1 bug
- CLOSED
- 2
updated Jun 11, 2020
Error if no VirSorter results in AMR_MGE.R

#39 · created May 19, 2020 by Valentina Galata Paper review - Microbiome - 1 bug
- CLOSED
- 5
updated Mar 24, 2021
PlasFlow minimal contig length from config

#40 · created May 25, 2020 by Valentina Galata Paper review - Microbiome - 1 enhancement
- CLOSED
- 1
updated Jan 12, 2021

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