Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / aroneys/binchicken issues and pull requests

#152 - Update docs

Pull Request - State: closed - Opened by AroneyS 13 days ago

#151 - Run no genomes in lazy mode

Pull Request - State: closed - Opened by AroneyS about 1 month ago

#150 - Add precluster distances argument

Pull Request - State: closed - Opened by AroneyS about 1 month ago

#149 - Update snakemake

Pull Request - State: open - Opened by AroneyS about 1 month ago

#103 - doc thing

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

#100 - Add links and citation

Pull Request - State: closed - Opened by AroneyS 10 months ago

#99 - Update precluster branch

Pull Request - State: closed - Opened by AroneyS 11 months ago

#98 - Track emerge_fork

Pull Request - State: closed - Opened by AroneyS 11 months ago

#97 - Track sra_fork

Pull Request - State: open - Opened by AroneyS 11 months ago

#96 - Change name to binchicken

Pull Request - State: closed - Opened by AroneyS 11 months ago

#95 - Improve genome loading

Pull Request - State: closed - Opened by AroneyS 11 months ago

#94 - Update dependencies

Pull Request - State: closed - Opened by AroneyS 11 months ago

#93 - Snakefile improvements

Pull Request - State: closed - Opened by AroneyS 11 months ago

#92 - Kmer preclustering

Pull Request - State: closed - Opened by AroneyS 12 months ago

#91 - Update fork

Pull Request - State: closed - Opened by AroneyS 12 months ago

#90 - Update fork

Pull Request - State: closed - Opened by AroneyS 12 months ago

#89 - Add Aviary build to Ibis build

Pull Request - State: closed - Opened by AroneyS 12 months ago

#88 - Update fork

Pull Request - State: closed - Opened by AroneyS 12 months ago

#87 - Update fork

Pull Request - State: closed - Opened by AroneyS 12 months ago

#86 - Quality of life improvements

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

#85 - Update fork

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

#84 - Update fork

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

#83 - update fork

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

#82 - update fork

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

#81 - update fork

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

#80 - update fork

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

#79 - Fix using max recovery samples with single assembly

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

#78 - Update Aviary env

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

#77 - Update fork

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

#76 - Update fork

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

#75 - Add SingleM metapackage env var

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

#74 - Track emerge-fork

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

#73 - Track sra-cluster-fork

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

#72 - Update fork

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

#71 - Add input to restrict coassembly samples

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

#70 - Update dependencies

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

#69 - Update fork

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

#68 - Fix QC

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

#67 - Skip single-ended on rerun

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

#66 - Update fork

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

#65 - Update SingleM

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

#64 - Add more suffix options

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

#63 - Update polars to v0.19

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

#62 - Update fork

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

#61 - Prevent aviary recover output deletion

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

#60 - Update fork

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

#59 - Fix split sra downloads

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

#58 - Update fork

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

#57 - Separate read downloading

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

#56 - Update fork

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

#55 - Switch to Fastp QC

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

#54 - Update fork

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

#53 - Restrict polars threads in main

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

#52 - Update fork

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

#51 - Remove use of -- before target rule/file

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

#50 - Update fork

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

#49 - Remove bbduk qc filtering

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

#48 - Switch to cores arg for snakemake

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

#47 - update sra-cluster-fork

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

#46 - update kingfisher to v0.3.0

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

#45 - Filter out samples not present in forward input

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

#44 - Update sra-cluster-fork

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

#43 - Update sra-cluster-fork

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

#42 - Add coassemble arg

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

#41 - Update fork

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

#40 - Deduplicate contig names in incoming genomes for unmapping

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

#39 - Better snakemake cluster support

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

#38 - Fix _1 being used instead of .1

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

#37 - Support snakemake cluster

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

#36 - SRA downloading improvements

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

#35 - Add `--new-genome-singlem` argument to iterate

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

#34 - Update Aviary to v0.7.0

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

#33 - Fix aviary commands

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

#32 - Fix cluster graph memory

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

#31 - Update polars to v0.18.11

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

#30 - Improve iterate

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

#29 - Update evaluate

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

#28 - Add new genomes input

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

#27 - Separate single-assembly from no-genomes

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

#26 - Fix target elusive memory issues

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

#25 - Add build subcommand

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

#24 - Update aviary v0.6.0

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

#23 - Update polars v0.18

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

#22 - Switch to greedy algorithm

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

#21 - Fix conda env versions

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

#20 - Add aligned fraction unmapping

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

#19 - Check for interleaved SRA

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

#18 - Update unmap

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

#17 - Add taxa of interest filtering to query_processing

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

#16 - Account for nontarget unbinned sequences in evaluate script

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

#15 - Remove S3.18.EIF_2_alpha sequences

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

#14 - Add no genomes argument

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

#13 - Stream graph communities

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

#12 - Switch from pandas to polars

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

#11 - Add argument to select specific coassemblies to unmap

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

#10 - Change name to Ibis

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

#9 - account for all clusters being filtered out

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

#8 - Improve unmapping

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

#7 - Fix evaluate errors with multiple coassemblies

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

#6 - Evaluate improvements

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