peterjc thapbi-pict issues

peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool

https://thapbi-pict.readthedocs.io/

MIT License

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[pre-commit.ci] autoupdate

#633 pre-commit-ci[bot] closed 4 days ago
0
Dual marker default DB (ITS1 and rps10)

#632 peterjc opened 5 days ago
0
Optional -k / --markers to pipeline and prepare-reads

#631 peterjc closed 5 days ago
0
Adding fifth synthetic control to default DB

#630 peterjc closed 5 days ago
0
Fix cutadapt stdin failures on AppVeyor (Windows)

#629 peterjc closed 2 weeks ago
0
Confirm bootstrapped DB unchanged without git-diff

#628 peterjc closed 2 weeks ago
0
Tests failing on AppVeyor

#627 peterjc closed 2 weeks ago
13
CircleCI timing out during database bootstrapping

#626 peterjc closed 2 weeks ago
0
[pre-commit.ci] autoupdate

#625 pre-commit-ci[bot] closed 4 weeks ago
3
Stop using Excel freeze-panes

#624 peterjc closed 1 month ago
0
[pre-commit.ci] autoupdate

#623 pre-commit-ci[bot] closed 2 months ago
1
Refresh unknowns.fasta, Oomycota_ITS1_obs.fasta, and thus DB

#622 peterjc closed 2 months ago
0
Further work on updating Oomycota_ITS1_obs.fasta

#621 peterjc closed 2 months ago
0
Refresh unknowns.fasta and thus Oomycota_ITS1_obs.fasta and DB

#620 peterjc closed 2 months ago
0
Update NCBI import as of 2024-04-12

#619 peterjc closed 2 months ago
0
Our four synthetic controls now have accessions PP407413-PP407416

#618 peterjc closed 2 months ago
0
[pre-commit.ci] autoupdate

#617 pre-commit-ci[bot] closed 3 months ago
0
Refresh API doc index

#616 peterjc closed 3 months ago
2
Migrate most flake8 plugins to ruff implementations

#615 peterjc closed 3 months ago
0
Add shellcheck and shfmt to the pre-commit configuration

#614 peterjc closed 3 months ago
0
Use PP407413-PP407416 for our synthentic controls

#613 peterjc closed 2 months ago
1
ftp.ncbi.nih.gov --> ftp.ncbi.nlm.nih.gov

#612 peterjc closed 3 months ago
0
Explore dbotu3 in sample-tally as UNOISE alternative

#611 peterjc opened 3 months ago
0
Restore Python 3.8 support (and test this)

#610 peterjc closed 3 months ago
1
Heuristics for missing genus in SINTAX species entry

#609 peterjc closed 4 months ago
0
BIOM output from sample-tally & harmonise ASV naming in output files

#608 peterjc closed 4 months ago
0
Use ruff for import sorting

#607 peterjc closed 4 months ago
0
[pre-commit.ci] autoupdate

#606 pre-commit-ci[bot] closed 4 months ago
0
Adjust the metadata counts in the read report

#605 peterjc closed 4 months ago
0
Expand classifiers with distance based 1s7g to 1s9g methods

#604 peterjc closed 4 months ago
0
Change sample report 'Unique' column to number of unique ASVs

#603 peterjc closed 4 months ago
0
Fix extra "blank" fields in the reports for unsequenced samples

#602 peterjc closed 4 months ago
1
Sample report "Unique" column is misleading

#601 peterjc closed 4 months ago
0
Use thousands separators in Excel output

#600 peterjc closed 4 months ago
0
Use thousands separator for read counts in the Excel reports

#599 peterjc closed 4 months ago
1
Don't import species names with semi-colon in them

#598 peterjc closed 4 months ago
0
Store deeper taxonomy?

#597 peterjc opened 4 months ago
0
Add 15 "novel" Phytophthora species

#596 peterjc closed 5 months ago
1
[pre-commit.ci] autoupdate

#595 pre-commit-ci[bot] closed 5 months ago
0
Update to Feb 2024 NCBI taxonomy

#594 peterjc closed 5 months ago
0
Adding three more Phytophthora species to the curated set

#593 peterjc closed 5 months ago
0
Fix year for Catala et al. (2015) novel species

#592 peterjc closed 5 months ago
0
Fix year 2018 to 2015 for Catala et al. novel species

#591 peterjc closed 4 months ago
1
Treat P. cambivora as a synonym of P. x cambivora

#590 peterjc closed 5 months ago
0
Phytophthora cambivora -> Phytophthora x cambivora

#589 peterjc closed 5 months ago
0
Update NCBI import

#588 peterjc closed 5 months ago
0
Adding new ON130151.X Peronospora gaponenkoae to DB

#587 peterjc closed 5 months ago
1
Adding a Pythiogeton proliferatum sequence to curated DB

#586 peterjc closed 5 months ago
1
Adding some currated Peronosclerospora to default DB

#585 peterjc closed 5 months ago
2
Remove 'Phytophthora austrocedri' workaround

#584 peterjc closed 5 months ago
1