OLC-Bioinformatics/ConFindr issues and pull requests

#60 - Add to GRDI-AMR.com

Issue - State: closed - Opened by chapb 4 months ago - 2 comments

#59 - ConFindr error with trash data

Issue - State: open - Opened by happykhan 8 months ago - 1 comment

#58 - Missing PercentContam in cgMLST mode

Issue - State: closed - Opened by gputzel 10 months ago - 1 comment

#57 - Didn't save genus-specific databases to temporary directory

Issue - State: open - Opened by chen1i6c04 11 months ago

#56 - Can't get oauth_verifier

Issue - State: closed - Opened by chen1i6c04 11 months ago - 3 comments

#55 - Error installing DB

Issue - State: open - Opened by shlomobl 11 months ago - 1 comment

#54 - Fix parsing of FASTQ files with adapter sequences in headers

Issue - State: open - Opened by pcrxn 12 months ago
Labels: bug

#53 - Add Biocontainers Docker image to README and documentation

Issue - State: open - Opened by pcrxn 12 months ago
Labels: enhancement

#52 - KeyError

Issue - State: closed - Opened by jonathho 12 months ago - 9 comments

#51 - Docker Image

Issue - State: closed - Opened by MrTomRod about 1 year ago - 4 comments
Labels: enhancement

#50 - Fix CircleCI testing

Pull Request - State: closed - Opened by pcrxn over 1 year ago

#49 - KeyError when running ConFindr v0.8.1 on test dataset

Issue - State: closed - Opened by pcrxn over 1 year ago - 2 comments
Labels: bug

#48 - Circleci project setup

Pull Request - State: closed - Opened by pcrxn over 1 year ago
Labels: enhancement

#47 - v0.8.1

Pull Request - State: closed - Opened by pcrxn over 1 year ago
Labels: bug, enhancement, dependencies

#46 - Error while downloading cgMLST

Issue - State: closed - Opened by ryobon-dev over 1 year ago - 2 comments

#45 - Error while running confinder

Issue - State: closed - Opened by ryobon-dev over 1 year ago - 3 comments

#44 - E. coli db issue

Issue - State: closed - Opened by elina2410 almost 2 years ago - 2 comments

#43 - confindr_database_setup

Issue - State: closed - Opened by joergFLI almost 2 years ago - 4 comments

#42 - Error when running ConFindr on unusual oganisms

Issue - State: closed - Opened by cjdgug almost 2 years ago - 9 comments

#41 - Issues setting up DB

Issue - State: closed - Opened by juliofdiaz about 2 years ago - 9 comments

#40 - Error while running kma

Issue - State: closed - Opened by rafalkolenda about 2 years ago - 5 comments

#39 - Wrong phred score base with low quality Nanopore data

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

#38 - bbtools error

Issue - State: closed - Opened by annacorreia over 2 years ago - 3 comments

#37 - Bump numpy from 1.21.0 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#36 - Running ConFindr with weird internet access

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

#35 - Hardcoded path to refseq.msh does no exists

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

#34 - Bump numpy from 1.15.1 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#33 - Request details on programmatic database setup for confindr

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

#32 - problem installing the rMLST database with confindr 0.7.4

Issue - State: closed - Opened by ysevel over 2 years ago - 7 comments

#31 - Save access token to permit automation database download

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

#30 - ConFindr :: problem with bbtools

Issue - State: closed - Opened by EricDeveaud almost 3 years ago - 16 comments

#29 - DB indexing (samtools, kma):: DB location not writable

Issue - State: closed - Opened by EricDeveaud almost 3 years ago - 5 comments
Labels: enhancement

#28 - rMLST databases are not freely available

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

#27 - problems with confindr rMLSt database

Issue - State: closed - Opened by KasiaTluscik almost 3 years ago - 4 comments

#26 - SamtoolsError

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

#25 - Installation errors using conda/bioconda

Issue - State: closed - Opened by ajkarloss over 3 years ago - 3 comments

#24 - Bump py from 1.5.2 to 1.10.0

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#23 - Trimmed or Untrimmed reads?

Issue - State: closed - Opened by vappiah over 3 years ago - 2 comments

#22 - Single-end/Paired-end results discrepancies

Issue - State: closed - Opened by fredericQC over 3 years ago - 3 comments

#21 - Error when attempting to run ConFindr on sample

Issue - State: closed - Opened by connerse almost 4 years ago - 3 comments

#20 - ConFindr conda install dependencies can't be solved

Issue - State: closed - Opened by crashfrog about 4 years ago - 2 comments

#19 - input fasta

Issue - State: closed - Opened by mdabalkey about 4 years ago - 8 comments

#18 - Error when running confindr.py

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

#17 - Keep running when rmlst.fasta is empty

Issue - State: closed - Opened by duceppemo almost 5 years ago - 1 comment

#16 - KMA issue

Issue - State: closed - Opened by Lcornet about 5 years ago - 3 comments

#15 - PackagesNotFoundError

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

#14 - kma exit status issue

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

#13 - Develop non-rMLST databases for priority pathogens

Issue - State: closed - Opened by lowandrew over 5 years ago - 1 comment
Labels: enhancement, high priority

#12 - Problems with confindr 0.5.1 install via conda

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

#11 - Error: Encountered error when attempting to run ConFindr on sample X. Skipping...

Issue - State: closed - Opened by ammaraziz almost 6 years ago - 3 comments

#10 - Consider using SeqIO.index instead of looping through the whole FASTA.

Issue - State: closed - Opened by andersgs almost 6 years ago - 3 comments
Labels: enhancement

#9 - DB location not writable

Issue - State: closed - Opened by andersgs almost 6 years ago - 3 comments
Labels: enhancement

#8 - Xmx option

Issue - State: closed - Opened by antunderwood almost 6 years ago - 4 comments

#7 - Consistent order for base depth counts in _contamination output files

Issue - State: closed - Opened by lowandrew almost 6 years ago - 2 comments
Labels: enhancement

#6 - Merge pull request #2 from lowandrew/master

Pull Request - State: closed - Opened by lowandrew almost 6 years ago

#5 - base fraction cutoff

Pull Request - State: closed - Opened by antunderwood almost 6 years ago - 2 comments

#4 - incorrect SNP counting?

Issue - State: closed - Opened by antunderwood almost 6 years ago - 2 comments

#3 - TypeError: count() got an unexpected keyword argument 'contig'

Issue - State: closed - Opened by ammaraziz almost 6 years ago - 6 comments

#2 - Merge pull request #1 from lowandrew/master

Pull Request - State: closed - Opened by lowandrew almost 7 years ago

#1 - Created pipeline_contamination_detection.py to allow pipeline integration

Pull Request - State: closed - Opened by adamkoziol almost 7 years ago

GitHub / OLC-Bioinformatics/ConFindr issues and pull requests