OLC-Bioinformatics/ConFindr issues and pull requests

#74 - KeyError while processing reads on Sanger fastq format

Issue - State: closed - Opened by hgrandjean 4 months ago - 7 comments

#73 - Version 0.7.4 - incongruent results between Conda and Biocontainers

Issue - State: closed - Opened by marchoeppner 5 months ago - 6 comments

#72 - v0.8.2

Pull Request - State: closed - Opened by pcrxn 6 months ago
Labels: bug, enhancement

#71 - Update instructions for obtaining PubMLST access

Pull Request - State: closed - Opened by pcrxn 6 months ago

#70 - Fix and expand parsing of FASTQ record headers for paired-end Illumina reads

Pull Request - State: closed - Opened by pcrxn 6 months ago
Labels: bug

#69 - Use secure HTTP headers for PubMLST URLs

Pull Request - State: closed - Opened by pcrxn 6 months ago

#68 - Use secure HTTP headers for PubMLST URLs

Pull Request - State: closed - Opened by pcrxn 6 months ago
Labels: bug

#67 - confindr_database_download: No request token specified

Issue - State: closed - Opened by pcrxn 6 months ago
Labels: bug, high priority

#66 - Support for ONT data

Issue - State: closed - Opened by marchoeppner 7 months ago

#65 - Fix Issue #57

Pull Request - State: closed - Opened by pcrxn 8 months ago - 1 comment
Labels: bug

#64 - Current test dataset is packaged in .zip format on Figshare (not .tar.gz)

Issue - State: closed - Opened by pcrxn 9 months ago - 1 comment
Labels: bug

#63 - Bug load fastq records

Issue - State: closed - Opened by miliskato 9 months ago - 3 comments

#62 - PubMLST now allows automated creation of personal API keys

Pull Request - State: closed - Opened by kjolley 9 months ago

#61 - libgfortran.so.3: cannot open shared object file: No such file or directory

Issue - State: closed - Opened by AKWB 11 months ago - 2 comments

#60 - Add to GRDI-AMR.com

Issue - State: closed - Opened by chapb about 1 year ago - 2 comments

#59 - ConFindr error with trash data

Issue - State: open - Opened by happykhan over 1 year ago - 1 comment

#58 - Missing PercentContam in cgMLST mode

Issue - State: closed - Opened by gputzel over 1 year ago - 1 comment

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

Issue - State: closed - Opened by chen1i6c04 over 1 year ago - 1 comment
Labels: bug

#56 - Can't get oauth_verifier

Issue - State: closed - Opened by chen1i6c04 over 1 year ago - 3 comments

#55 - Error installing DB

Issue - State: closed - Opened by shlomobl almost 2 years ago - 1 comment

#54 - Fix parsing of paired-end FASTQ files

Issue - State: closed - Opened by pcrxn almost 2 years ago - 1 comment
Labels: bug

#53 - Add Biocontainers Docker image to README and documentation

Issue - State: open - Opened by pcrxn almost 2 years ago
Labels: enhancement

#52 - KeyError

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

#51 - Docker Image

Issue - State: closed - Opened by MrTomRod almost 2 years ago - 4 comments
Labels: enhancement

#50 - Fix CircleCI testing

Pull Request - State: closed - Opened by pcrxn about 2 years ago

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

Issue - State: closed - Opened by pcrxn about 2 years ago - 2 comments
Labels: bug

#48 - Circleci project setup

Pull Request - State: closed - Opened by pcrxn about 2 years ago
Labels: enhancement

#47 - v0.8.1

Pull Request - State: closed - Opened by pcrxn about 2 years ago
Labels: bug, enhancement, dependencies

#46 - Error while downloading cgMLST

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

#45 - Error while running confinder

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

#44 - E. coli db issue

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

#43 - confindr_database_setup

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

#42 - Error when running ConFindr on unusual oganisms

Issue - State: closed - Opened by cjdgug almost 3 years ago - 9 comments

#41 - Issues setting up DB

Issue - State: closed - Opened by juliofdiaz almost 3 years ago - 9 comments

#40 - Error while running kma

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

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

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

#38 - bbtools error

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

#37 - Bump numpy from 1.21.0 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 2 comments
Labels: dependencies

#36 - Running ConFindr with weird internet access

Issue - State: closed - Opened by lskatz about 3 years ago - 2 comments

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

Issue - State: closed - Opened by bjhall over 3 years ago - 1 comment

#34 - Bump numpy from 1.15.1 to 1.21.0

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

#33 - Request details on programmatic database setup for confindr

Issue - State: closed - Opened by bala-ruokavirasto over 3 years ago - 5 comments

#32 - problem installing the rMLST database with confindr 0.7.4

Issue - State: closed - Opened by ysevel over 3 years ago - 7 comments

#31 - Save access token to permit automation database download

Pull Request - State: closed - Opened by braffes over 3 years ago

#30 - ConFindr :: problem with bbtools

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

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

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

#28 - rMLST databases are not freely available

Pull Request - State: closed - Opened by kjolley almost 4 years ago

#27 - problems with confindr rMLSt database

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

#26 - SamtoolsError

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

#25 - Installation errors using conda/bioconda

Issue - State: closed - Opened by ajkarloss about 4 years ago - 3 comments

#24 - Bump py from 1.5.2 to 1.10.0

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago
Labels: dependencies

#23 - Trimmed or Untrimmed reads?

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

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

Issue - State: closed - Opened by fredericQC over 4 years ago - 3 comments

#21 - Error when attempting to run ConFindr on sample

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

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

Issue - State: closed - Opened by crashfrog almost 5 years ago - 2 comments

#19 - input fasta

Issue - State: closed - Opened by mdabalkey almost 5 years ago - 8 comments

#18 - Error when running confindr.py

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

#17 - Keep running when rmlst.fasta is empty

Issue - State: closed - Opened by duceppemo almost 6 years ago - 1 comment

#16 - KMA issue

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

#15 - PackagesNotFoundError

Issue - State: closed - Opened by wjidea about 6 years ago - 2 comments

#14 - kma exit status issue

Issue - State: closed - Opened by pkmitchell about 6 years ago - 5 comments
Labels: bug

#13 - Develop non-rMLST databases for priority pathogens

Issue - State: closed - Opened by lowandrew over 6 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 6 years ago - 2 comments

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

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

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

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

#9 - DB location not writable

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

#8 - Xmx option

Issue - State: closed - Opened by antunderwood almost 7 years ago - 4 comments

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

Issue - State: closed - Opened by lowandrew almost 7 years ago - 2 comments
Labels: enhancement

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

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

#5 - base fraction cutoff

Pull Request - State: closed - Opened by antunderwood almost 7 years ago - 2 comments

#4 - incorrect SNP counting?

Issue - State: closed - Opened by antunderwood almost 7 years ago - 2 comments

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

Issue - State: closed - Opened by ammaraziz almost 7 years ago - 6 comments

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

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

#1 - Created pipeline_contamination_detection.py to allow pipeline integration

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

GitHub / OLC-Bioinformatics/ConFindr issues and pull requests