peterjc/thapbi-pict issues and pull requests

#645 - Return Session instance from connect_to_db

Pull Request - State: closed - Opened by peterjc 2 months ago

#644 - Dicard zero-abundance ASV caused by requires-metadata

Pull Request - State: closed - Opened by peterjc 2 months ago

#643 - Option to filter reports to only samples of interest via metadata

Pull Request - State: closed - Opened by peterjc 2 months ago - 2 comments

#642 - More observed sequences for reference DB; Update NCBI taxonomy

Pull Request - State: closed - Opened by peterjc 2 months ago

#641 - [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 3 months ago

#640 - Curated sequences database updates

Pull Request - State: closed - Opened by peterjc 3 months ago - 3 comments

#639 - Update to use Aug 2024 NCBI taxonomy

Pull Request - State: closed - Opened by peterjc 3 months ago

#638 - Test breaking due to bad combination of NetworkX and pydot

Issue - State: closed - Opened by peterjc 3 months ago - 1 comment

#637 - Avoid bad combination of NetworkX and pydot

Pull Request - State: closed - Opened by peterjc 3 months ago

#636 - Switch from miniconda to miniforge

Pull Request - State: closed - Opened by peterjc 3 months ago - 1 comment

#635 - [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 3 months ago - 4 comments

#634 - Use our fifth synthetic control in the default ITS1 DB

Pull Request - State: closed - Opened by peterjc 4 months ago - 1 comment

#633 - [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#632 - Dual marker default DB (ITS1 and rps10)

Pull Request - State: open - Opened by peterjc 5 months ago

#631 - Optional -k / --markers to pipeline and prepare-reads

Pull Request - State: closed - Opened by peterjc 5 months ago

#630 - Adding fifth synthetic control to default DB

Pull Request - State: closed - Opened by peterjc 5 months ago

#629 - Fix cutadapt stdin failures on AppVeyor (Windows)

Pull Request - State: closed - Opened by peterjc 5 months ago

#628 - Confirm bootstrapped DB unchanged without git-diff

Pull Request - State: closed - Opened by peterjc 5 months ago

#627 - Tests failing on AppVeyor

Issue - State: closed - Opened by peterjc 5 months ago - 13 comments

#626 - CircleCI timing out during database bootstrapping

Issue - State: closed - Opened by peterjc 5 months ago

#625 - [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago - 3 comments

#624 - Stop using Excel freeze-panes

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

#623 - [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago - 1 comment

#622 - Refresh unknowns.fasta, Oomycota_ITS1_obs.fasta, and thus DB

Pull Request - State: closed - Opened by peterjc 7 months ago

#621 - Further work on updating Oomycota_ITS1_obs.fasta

Pull Request - State: closed - Opened by peterjc 7 months ago

#620 - Refresh unknowns.fasta and thus Oomycota_ITS1_obs.fasta and DB

Pull Request - State: closed - Opened by peterjc 7 months ago

#619 - Update NCBI import as of 2024-04-12

Pull Request - State: closed - Opened by peterjc 7 months ago

#618 - Our four synthetic controls now have accessions PP407413-PP407416

Pull Request - State: closed - Opened by peterjc 7 months ago

#617 - [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago

#616 - Refresh API doc index

Pull Request - State: closed - Opened by peterjc 8 months ago - 2 comments

#615 - Migrate most flake8 plugins to ruff implementations

Pull Request - State: closed - Opened by peterjc 8 months ago

#614 - Add shellcheck and shfmt to the pre-commit configuration

Pull Request - State: closed - Opened by peterjc 8 months ago

#613 - Use PP407413-PP407416 for our synthentic controls

Issue - State: closed - Opened by peterjc 8 months ago - 1 comment

#612 - ftp.ncbi.nih.gov --> ftp.ncbi.nlm.nih.gov

Pull Request - State: closed - Opened by peterjc 8 months ago

#611 - Explore dbotu3 in sample-tally as UNOISE alternative

Issue - State: open - Opened by peterjc 8 months ago
Labels: enhancement