norwegianveterinaryinstitute/alppaca issues and pull requests

#120 - Panaroo core gene alignment issue

Issue - State: open - Opened by hkaspersen 8 months ago - 4 comments
Labels: bug

#119 - Create over-arching workflow to run several tracks at once

Issue - State: open - Opened by hkaspersen 11 months ago
Labels: enhancement

#119 - Create over-arching workflow to run several tracks at once

Issue - State: open - Opened by hkaspersen 11 months ago
Labels: enhancement

#118 - Version 2.3.2

Pull Request - State: closed - Opened by hkaspersen 11 months ago - 1 comment

#118 - Version 2.3.2

Pull Request - State: closed - Opened by hkaspersen 11 months ago - 1 comment

#117 - fix input to parsnp

Issue - State: closed - Opened by hkaspersen 12 months ago
Labels: bug

#116 - Correct the Gubbins conda version

Issue - State: closed - Opened by hkaspersen 12 months ago

#116 - Correct the Gubbins conda version

Issue - State: closed - Opened by hkaspersen 12 months ago

#115 - bootstrap display on branches

Issue - State: open - Opened by evezeyl 12 months ago - 2 comments
Labels: enhancement

#114 - Patch 2.3.1

Pull Request - State: closed - Opened by hkaspersen about 1 year ago

#114 - Patch 2.3.1

Pull Request - State: closed - Opened by hkaspersen about 1 year ago

#113 - Add gff files as optional output in core gene track

Issue - State: closed - Opened by hkaspersen about 1 year ago
Labels: enhancement

#112 - Update ParSNP to version 2.0.0

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

#111 - automation clustering - level selection and CC/simi

Issue - State: open - Opened by evezeyl about 1 year ago
Labels: enhancement

#110 - Pull request for version 2.3.0

Pull Request - State: closed - Opened by hkaspersen about 1 year ago

#109 - implement the new version of gubbins - that can be sed fixed

Issue - State: closed - Opened by evezeyl about 1 year ago - 2 comments
Labels: enhancement

#108 - identity thresholds in panaroo

Issue - State: closed - Opened by snogu over 1 year ago
Labels: enhancement

#107 - gene presence absence table

Issue - State: closed - Opened by snogu over 1 year ago
Labels: enhancement

#106 - Review output hamming distances

Issue - State: closed - Opened by evezeyl over 1 year ago
Labels: enhancement

#105 - Add monocytogenes scheme to MLST image - maybe

Issue - State: closed - Opened by evezeyl over 1 year ago - 3 comments
Labels: bug

#104 - Added support for running pipeline with apptainer

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#103 - Add Apptainer profile

Issue - State: closed - Opened by hkaspersen almost 2 years ago

#102 - Check the new version of chewBBACA

Issue - State: closed - Opened by hkaspersen almost 2 years ago
Labels: enhancement

#101 - wiki - clarify - the mapping analysis example

Issue - State: closed - Opened by evezeyl almost 2 years ago - 1 comment
Labels: documentation, enhancement

#100 - Merge pull request #99 from NorwegianVeterinaryInstitute/dev

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#99 - cgMLST update

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#98 - added test data schema for cgmlst

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#97 - fixed typo

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#96 - Adding the cgmlst track and CI test

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#95 - Adding the cgmlst track

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#94 - Add filtering check step for cgmlst track

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

#93 - Normalize distance for cgMLST

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

#92 - latest image chewbbaca

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

#91 - snp-dists -m option please

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

#90 - Merge pull request #89 from NorwegianVeterinaryInstitute/dev

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#90 - Merge pull request #89 from NorwegianVeterinaryInstitute/dev

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#89 - Added unaligned regions as output from parsnp

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#89 - Added unaligned regions as output from parsnp

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#88 - Add option for outputting unaligned regions

Issue - State: closed - Opened by hkaspersen almost 2 years ago - 1 comment
Labels: enhancement

#88 - Add option for outputting unaligned regions

Issue - State: closed - Opened by hkaspersen almost 2 years ago - 1 comment
Labels: enhancement

#87 - logo and readme

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#87 - logo and readme

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#86 - Add option for quick phylogeny

Issue - State: open - Opened by hkaspersen almost 2 years ago - 1 comment
Labels: enhancement

#86 - Add option for quick phylogeny

Issue - State: closed - Opened by hkaspersen almost 2 years ago - 1 comment
Labels: enhancement

#85 - Merge pull request #84 from NorwegianVeterinaryInstitute/dev

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#85 - Merge pull request #84 from NorwegianVeterinaryInstitute/dev

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#84 - Updated figure

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#84 - Updated figure

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#83 - dev

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#83 - dev

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#82 - updated manifest version

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#82 - updated manifest version

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#81 - ANI track added

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#81 - ANI track added

Pull Request - State: closed - Opened by hkaspersen almost 2 years ago

#80 - added modules for ANI track, as of issue #43

Pull Request - State: closed - Opened by evezeyl almost 2 years ago

#80 - added modules for ANI track, as of issue #43

Pull Request - State: closed - Opened by evezeyl almost 2 years ago

#79 - Create ANI_Report.R

Pull Request - State: closed - Opened by evezeyl almost 2 years ago

#79 - Create ANI_Report.R

Pull Request - State: closed - Opened by evezeyl almost 2 years ago

#78 - ALPPACA - FASTANI - wrap script : clean fastANI results + statistics + tree that can be viewed

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