Ecosyste.ms: Issues

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

GitHub / dib-lab/genome-grist issues and pull requests

#215 - locked directory error message

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

#214 - [MRG] fix mapping notebook to properly handle a single genome

Pull Request - State: closed - Opened by ctb over 2 years ago

#213 - [MRG] switch to gzipped sourmash input/output files

Pull Request - State: closed - Opened by ctb over 2 years ago - 1 comment

#212 - add an `unlock` command and/or trap CTRL-C and unlock

Issue - State: open - Opened by ctb over 2 years ago

#211 - [MRG] add an initial summary of output files and their contents

Pull Request - State: closed - Opened by ctb over 2 years ago - 1 comment

#210 - create a bulk assembly rule?

Issue - State: open - Opened by ctb over 2 years ago

#209 - [MRG] change column names in mapping summary files; add count of mapped reads.

Pull Request - State: closed - Opened by ctb over 2 years ago - 1 comment

#208 - add information about number of reads to mapping outputfiles

Issue - State: closed - Opened by ctb over 2 years ago - 1 comment

#207 - document mapping outputs and summary file columns

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

#206 - document output files and their contents

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

#205 - stop repeatedly loading gather CSV output!

Issue - State: closed - Opened by ctb over 2 years ago

#204 - error with gather and picklists using private metagenomes

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

#203 - add pip install screed to instructions?

Issue - State: open - Opened by jessicalumian over 2 years ago - 1 comment

#202 - update genome-grist to take advantage of new sourmash features

Issue - State: open - Opened by ctb over 2 years ago

#201 - out-of-memory error

Issue - State: open - Opened by jeanzzhao over 2 years ago - 2 comments
Labels: documentation

#200 - [MRG] fix exit codes from genome-grist CLI

Pull Request - State: closed - Opened by ctb over 2 years ago

#199 - [MRG] remove abundance trimming from the default genome-grist workflow

Pull Request - State: closed - Opened by ctb over 2 years ago

#198 - document snakemake cmd line additions, suggest `-k` as default

Issue - State: open - Opened by ctb over 2 years ago - 1 comment

#197 - should we turn off read trimming/trim-low-abund, or make it optional?

Issue - State: closed - Opened by ctb over 2 years ago - 8 comments

#196 - can we report snakemake errors in a nicer summary way?

Issue - State: open - Opened by ctb over 2 years ago

#195 - [MRG] provide a better error message for empty prefetch; upgrade sourmash versions

Pull Request - State: closed - Opened by ctb over 2 years ago - 1 comment

#194 - genome-grist failing with empty prefetch_csv

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

#191 - trim-low-abund defaults to a k-mer size of 32

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

#190 - Generic StreamReadError error

Issue - State: open - Opened by hehouts over 2 years ago - 4 comments

#189 - failing on step "Run Gather"

Issue - State: closed - Opened by hehouts over 2 years ago - 5 comments

#188 - [MRG] Allow everything _but_ hyphens and periods in sample names

Pull Request - State: closed - Opened by ctb almost 3 years ago

#187 - hyphens in sample names causing "snakemake invocation error"

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

#181 - [MRG] Speed up `copy_local_genomes.py` with symbolic links

Pull Request - State: closed - Opened by mr-eyes almost 3 years ago - 5 comments

#159 - [WIP] add rules for protein mapping

Pull Request - State: open - Opened by bluegenes about 3 years ago - 1 comment

#154 - How to use grist with my own files

Issue - State: closed - Opened by padbc about 3 years ago - 12 comments

#141 - revisit/discuss genome-grist k-mer trimming

Issue - State: open - Opened by ctb about 3 years ago - 1 comment
Labels: faq

#138 - investigate hard links or symlinks for private genome collections

Issue - State: closed - Opened by ctb about 3 years ago

#22 - Add miscellaneous functionality

Pull Request - State: closed - Opened by ctb about 4 years ago