Issues · Laura Denies / PathoFact

New issue

Reduce output size 2 of 4 tasks completed

#45 · created Jun 08, 2020 by Valentina Galata Paper review - Microbiome - 1 clean-up enhancement
- CLOSED
- 0
updated Jun 22, 2020
Output format 2 of 2 tasks completed

#48 · created Jun 08, 2020 by Valentina Galata Paper review - Microbiome - 1 enhancement
- CLOSED
- 0
updated Jun 22, 2020
Update SignalP

#35 · created May 05, 2020 by Valentina Galata Paper review - Microbiome - 1 enhancement
- CLOSED
- 0
updated Jun 22, 2020
DeepARG - parameters in config file

#44 · created Jun 08, 2020 by Valentina Galata Paper review - Microbiome - 1 enhancement
- CLOSED
- 0
updated Jun 22, 2020
Update deeparg installation

#51 · created Jun 12, 2020 by Laura Denies bug
- CLOSED
- 0
updated Jun 18, 2020
Add RGI (AMR prediction) 5 of 5 tasks completed

#43 · created Jun 08, 2020 by Valentina Galata Paper review - Microbiome - 1 enhancement
- CLOSED
- 1
updated Jun 18, 2020
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
Add Prodigal to Pipeline

#50 · created Jun 10, 2020 by Laura Denies
- CLOSED
- 0
updated Jun 11, 2020
Replace SeqKit

#49 · created Jun 08, 2020 by Valentina Galata Paper review - Microbiome - 1 bug dependencies
- CLOSED
- 1
updated Jun 11, 2020
Snakemake: use && or || to concat CMDs in rules

#10 · created Apr 16, 2020 by Valentina Galata enhancement
- 0
updated Jun 08, 2020
intallation with docker/singularity

#42 · created May 27, 2020 by soilmicrobiome discussion enhancement
- 0
updated Jun 08, 2020
IMPiris: log files 2 of 4 tasks completed

#7 · created Apr 15, 2020 by Valentina Galata IMP
- CLOSED
- 1
updated May 05, 2020
IMPiris: test data

#9 · created Apr 15, 2020 by Valentina Galata IMP
- CLOSED
- 1
updated May 05, 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: 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
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: give snakemake files an extension

#18 · created Apr 20, 2020 by Valentina Galata spring-clean clean-up
- CLOSED
- 1
- 0
updated Apr 24, 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: all scripts in scripts/ 2 of 2 tasks completed

#15 · created Apr 20, 2020 by Valentina Galata spring-clean clean-up
- CLOSED
- 0
updated Apr 23, 2020