NBChub/bgcflow issues and pull requests

#100 - Error in extract_ncbi_information if only custom dataset is present

Issue - State: closed - Opened by OmkarSaMo over 2 years ago - 3 comments
Labels: bug

#99 - Fix: Simplify creation of user defined prokka-db

Pull Request - State: closed - Opened by matinnuhamunada over 2 years ago - 7 comments

#98 - Add Checkm feature

Issue - State: closed - Opened by OmkarSaMo over 2 years ago - 1 comment
Labels: enhancement

#97 - Checkm feature and minor fixes

Pull Request - State: closed - Opened by OmkarSaMo over 2 years ago - 2 comments

#96 - Merge from Main

Pull Request - State: closed - Opened by OmkarSaMo over 2 years ago

#95 - Merge from main

Pull Request - State: closed - Opened by OmkarSaMo over 2 years ago

#94 - Merge from Main

Pull Request - State: closed - Opened by OmkarSaMo over 2 years ago

#93 - Merge from Main

Pull Request - State: closed - Opened by OmkarSaMo over 2 years ago

#92 - Bug fixes

Pull Request - State: closed - Opened by matinnuhamunada over 2 years ago

#91 - Generate test to handle various input problems

Issue - State: closed - Opened by matinnuhamunada over 2 years ago - 3 comments
Labels: enhancement

#90 - Dealing with missing input column names

Issue - State: closed - Opened by matinnuhamunada over 2 years ago - 3 comments
Labels: bug

#89 - Reintroduce autoMLST and fix bugs

Pull Request - State: closed - Opened by matinnuhamunada over 2 years ago - 3 comments
Labels: bug, enhancement

#88 - auto-mlst changes the accession ids in the input file

Issue - State: closed - Opened by robertosanchezn over 2 years ago - 2 comments
Labels: bug

#87 - Error in gtdb - no attribute 'gtdb_taxonomy'

Issue - State: closed - Opened by ljdnielsen over 2 years ago - 15 comments
Labels: bug

#86 - Consider to start using tags for alpha version

Issue - State: closed - Opened by matinnuhamunada over 2 years ago
Labels: enhancement, question

#85 - Using Environment Modules

Issue - State: closed - Opened by matinnuhamunada over 2 years ago
Labels: enhancement

#84 - Post deployment scripts to manage installation

Issue - State: closed - Opened by matinnuhamunada over 2 years ago - 1 comment
Labels: enhancement

#83 - Merge from Main

Pull Request - State: closed - Opened by OmkarSaMo over 2 years ago

#82 - Merge changes from Main

Pull Request - State: closed - Opened by OmkarSaMo over 2 years ago

#81 - Merge to main

Pull Request - State: closed - Opened by OmkarSaMo over 2 years ago - 2 comments

#80 - Adding new project in the config file invoke re-runs

Issue - State: closed - Opened by matinnuhamunada over 2 years ago - 1 comment
Labels: bug

#79 - Error retrieving GTDB information

Issue - State: closed - Opened by matinnuhamunada over 2 years ago - 5 comments

#78 - Error in creating symbolic link while running BiGSCAPE

Issue - State: closed - Opened by OmkarSaMo over 2 years ago - 2 comments
Labels: bug

#77 - Error in rule format_gbk

Issue - State: closed - Opened by yzjie6 over 2 years ago - 20 comments
Labels: bug, question

#76 - Made most jobs independent

Pull Request - State: closed - Opened by matinnuhamunada over 2 years ago - 3 comments
Labels: enhancement

#75 - Error during creating conda antismash environment on local computer

Issue - State: closed - Opened by yzjie6 over 2 years ago - 1 comment
Labels: question

#74 - Rule extract_meta_prokka cause re-runs when sample.csv updated

Issue - State: closed - Opened by matinnuhamunada over 2 years ago
Labels: enhancement

#73 - Error reading fasta file information

Issue - State: closed - Opened by yzjie6 over 2 years ago - 1 comment
Labels: bug

#72 - Mapping back to NCBI refseq/genbank annotations

Issue - State: closed - Opened by OmkarSaMo over 2 years ago - 1 comment
Labels: enhancement

#71 - Project specific feature needs - brainstorming

Issue - State: closed - Opened by OmkarSaMo over 2 years ago
Labels: documentation, enhancement, question

#70 - Report logs output directory structure

Issue - State: closed - Opened by OmkarSaMo over 2 years ago - 4 comments
Labels: documentation, enhancement, question

#69 - feat: add reporting option

Pull Request - State: closed - Opened by OmkarSaMo over 2 years ago

#68 - SSL Certificate Error when accessing GTDB API

Issue - State: closed - Opened by matinnuhamunada over 2 years ago - 1 comment
Labels: bug

#67 - Notebook integration and processed data contents

Issue - State: closed - Opened by matinnuhamunada over 2 years ago - 5 comments
Labels: question

#66 - feat: add reporting option

Pull Request - State: closed - Opened by matinnuhamunada over 2 years ago - 1 comment
Labels: enhancement

#65 - NCBI genome download misses recently uploaded genomes

Issue - State: closed - Opened by OmkarSaMo over 2 years ago - 5 comments
Labels: bug

#64 - Config to adapt threads for computing resources

Issue - State: closed - Opened by matinnuhamunada over 2 years ago - 3 comments
Labels: enhancement

#63 - Binomial nomenclature - species vs species epithet

Issue - State: closed - Opened by matinnuhamunada over 2 years ago - 1 comment
Labels: question

#62 - BiG-SCAPE network files missing

Issue - State: closed - Opened by matinnuhamunada over 2 years ago - 2 comments
Labels: bug

#61 - Fix: enable roary and fixing small bugs

Pull Request - State: closed - Opened by matinnuhamunada over 2 years ago - 2 comments
Labels: bug

#60 - rule format_gbk invoke batch re-runs of antiSMASH when taxonomy file updated

Issue - State: closed - Opened by matinnuhamunada over 2 years ago - 2 comments
Labels: bug

#59 - roary missing in new release

Issue - State: closed - Opened by matinnuhamunada over 2 years ago
Labels: bug

#58 - Refrain using samples.csv for rule input

Issue - State: closed - Opened by matinnuhamunada over 2 years ago
Labels: bug

#57 - Snakemake --touch failed

Issue - State: closed - Opened by matinnuhamunada over 2 years ago - 3 comments
Labels: bug

#56 - fix: enable GTDB API parent taxon search from user defined genus

Pull Request - State: closed - Opened by matinnuhamunada over 2 years ago
Labels: bug, enhancement

#55 - BigSCAPE not working due to typo, correction in the code below of the bigscape.smk [identified by Omkar]

Issue - State: closed - Opened by MatissMaleckis over 2 years ago - 1 comment

#54 - gtdb_prep: error when closest reference placement is empty

Issue - State: closed - Opened by matinnuhamunada over 2 years ago - 2 comments

#53 - Feat: add RNAmmer for Prokka and GCA/GCF flexibility

Pull Request - State: closed - Opened by matinnuhamunada over 2 years ago - 2 comments
Labels: enhancement

#52 - Fasta filenames prevent run of Prokka

Issue - State: closed - Opened by MatissMaleckis over 2 years ago - 1 comment
Labels: documentation, question

#51 - Combine GTDB fetch rules

Issue - State: closed - Opened by OmkarSaMo over 2 years ago - 4 comments
Labels: bug, enhancement

#50 - NCBI download - Alternative download from Refseq or Genbank by assembly id

Issue - State: closed - Opened by MatissMaleckis over 2 years ago - 4 comments

#49 - Introducing Multiple Projects Run

Pull Request - State: closed - Opened by matinnuhamunada almost 3 years ago - 4 comments
Labels: enhancement

#48 - Introduce interactive config

Pull Request - State: closed - Opened by matinnuhamunada almost 3 years ago

#47 - Dev matinnu2

Pull Request - State: closed - Opened by matinnuhamunada almost 3 years ago

#46 - Create dummy genomes for speed testing

Issue - State: closed - Opened by matinnuhamunada almost 3 years ago - 4 comments
Labels: enhancement

#45 - Prokka: use PFAM database?

Issue - State: closed - Opened by matinnuhamunada almost 3 years ago - 3 comments
Labels: enhancement, question

#44 - Prokka: Rnammer does not found rRNA

Issue - State: closed - Opened by matinnuhamunada almost 3 years ago - 7 comments
Labels: bug, question

#43 - BGCflow v1 scope

Issue - State: closed - Opened by matinnuhamunada almost 3 years ago - 2 comments
Labels: documentation, question

#42 - Automlst wrapper needs to be fixed

Issue - State: closed - Opened by matinnuhamunada almost 3 years ago - 7 comments
Labels: bug

#41 - update github actions

Pull Request - State: closed - Opened by matinnuhamunada almost 3 years ago

#40 - Checkpoints in workflow for user interaction

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 2 comments
Labels: enhancement

#39 - Updates from main of refseq_masher, ncbi_meta, output tables

Pull Request - State: closed - Opened by OmkarSaMo almost 3 years ago

#38 - Merge from main branch

Pull Request - State: closed - Opened by OmkarSaMo almost 3 years ago

#37 - Git commit format discussion

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 2 comments
Labels: documentation, question

#36 - Consider using ancient marks for inputs to ignore timestamps

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 1 comment

#35 - Pull commits from main branch and resolve conflicts

Pull Request - State: closed - Opened by OmkarSaMo almost 3 years ago

#34 - feature: highlight input genomes on a GTDB tree

Issue - State: closed - Opened by robertosanchezn almost 3 years ago

#33 - feature: add SeqFu for genome assembly statistics

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 3 comments
Labels: enhancement

#32 - format gbk: Add GTDB taxonomy as metadata in Organism field

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 3 comments

#31 - merge to main branch v0.1.0

Pull Request - State: closed - Opened by OmkarSaMo almost 3 years ago

#30 - antismashDB: set up database server for individual projects

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 2 comments
Labels: enhancement

#29 - Create new rule for GTDB-tk if not found in GTDB

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 1 comment
Labels: bug, enhancement

#28 - schema update: change to json input from csv

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 2 comments

#27 - DevOps: Github Actions

Issue - State: closed - Opened by matinnuhamunada almost 3 years ago - 2 comments
Labels: enhancement

#26 - ncbi_meta: Update the assembly report parser

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 1 comment
Labels: bug

#25 - genbank: Annotate genbank output with GitHub version

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 1 comment

#24 - pull prokka fixes

Pull Request - State: closed - Opened by OmkarSaMo almost 3 years ago

#23 - prokka: use table for organism information

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 2 comments

#22 - Prokka genusdb

Pull Request - State: closed - Opened by OmkarSaMo almost 3 years ago

#21 - feature: CD-HIT for pangenome

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 1 comment
Labels: enhancement

#20 - feature: Antibiotic Resistant Target Seeker (ARTS)

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago
Labels: enhancement

#19 - feature: automlst tree for given genome dataset

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 1 comment

#18 - feature: add eggnog-mapper

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 5 comments

#17 - feature: Add kegg annotaitons

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 2 comments

#16 - feature: mlst to scan against traditional PubMLST typing schemes

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 1 comment

#15 - feature: refseq masher to find top 10 closest NCBI refseq genomes

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 1 comment
Labels: enhancement

#14 - src: add multi-processing features for python scripts

Issue - State: closed - Opened by matinnuhamunada almost 3 years ago - 2 comments
Labels: enhancement

#13 - src: make python scripts independent of snakemake params

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 2 comments

#12 - antismash : addtional directory with version supported by downstream analysis

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 4 comments
Labels: enhancement

#11 - user: create user input form to start up BGCflow

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 1 comment

#10 - gtdb: add separate rule file for gtdb

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 1 comment

#9 - patric: add rules to get fasta files from PATRIC database

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 1 comment
Labels: enhancement

#8 - prokka: add reference organisms list for Prokka database

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 7 comments
Labels: enhancement

#7 - ncbi: update metadata of genbank file post prokka

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 1 comment
Labels: enhancement

#6 - snakemake: new version (>6..8.0) indroduces path handling error

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 1 comment

#5 - bigslice: define the feature workflow

Issue - State: closed - Opened by OmkarSaMo almost 3 years ago - 2 comments
Labels: enhancement

#4 - Ppanggolin

Pull Request - State: closed - Opened by matinnuhamunada almost 3 years ago - 1 comment

#3 - update

Pull Request - State: closed - Opened by matinnuhamunada almost 3 years ago

#2 - fasta: merge all fasta files before running prokka

Issue - State: closed - Opened by OmkarSaMo about 3 years ago - 2 comments
Labels: enhancement

#1 - Add Prokka, AntiSMASH, and Roary

Pull Request - State: closed - Opened by matinnuhamunada about 3 years ago

GitHub / NBChub/bgcflow issues and pull requests