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Issues list

Revised index subcommands
#53 by bede was closed Dec 19, 2024
8 tasks done
2.0.0
1
Support stdout enhancement New feature or request
#52 by bede was closed Dec 19, 2024
2 tasks done
2.0.0
1
Catch mismatched read counts for paired input
#51 by bede was closed Dec 19, 2024 2.0.0
2
Add diagram of pipeline to README documentation Improvements or additions to documentation
#50 by bede was closed Dec 20, 2024
1
add mm39 genome index?
#49 by microbemarsh was closed Nov 29, 2024
5
Improve error message when an index is passed in an unexpected format documentation Improvements or additions to documentation enhancement New feature or request
#48 by bede was closed Nov 21, 2024 2.0.0
2
Clarify terminology with respect to unpaired/SE reads documentation Improvements or additions to documentation enhancement New feature or request
#47 by bede was closed Nov 21, 2024 2.0.0
2
Single end data, with a custom bowtie2 index results in 'missing index' error, but paired end data works fine
#46 by jfy133 was closed Nov 13, 2024
4
Hostile crashes if path has spaces in it bug Something isn't working
#45 by pvanheus was closed Oct 22, 2024 2.0.0
4
Update pinned aligner versions enhancement New feature or request
#44 by bede was closed Dec 19, 2024 2.0.0
2
Dockerfile fails: process "/bin/sh -c mamba env update -n base -f hostile/environment.yml" did not complete successfully bug Something isn't working packaging
#43 by dterumalai was closed Sep 12, 2024
3
Hostile with no options classifying different than --invert bug Something isn't working
#42 by jannikseidelQBiC was closed Dec 19, 2024 2.0.0
5
Allow adding of Illumina Casava 1.8 format entry to fastq headers enhancement New feature or request
#41 by charlesfoster was closed Dec 19, 2024 2.0.0
4
Automatically generate and cache minimap2 indexes to eliminate redundant indexing overhead enhancement New feature or request
#39 by bede was closed Dec 19, 2024
2
Mode: paired short read (Bowtie2) fails when index is provided as reference fasta file
#38 by Rohit-Satyam was closed May 31, 2024
1
Allow remote index repository to be overridden enhancement New feature or request
#37 by bede was closed Dec 19, 2024 2.0.0
2
Support accepting stdin instead of a specific filepath for single ended data enhancement New feature or request
#35 by BioWilko was closed Dec 19, 2024 2.0.0
4
Incorporating Single-End Short Read Data Support
#34 by Ackia was closed Apr 10, 2024
5
I think you can use --name (-n) on the mamba command line to override the environment name in the env file.
#33 by bdklahn was closed Apr 10, 2024
1
What's the best way to override the index download directory?
#32 by bdklahn was closed Apr 22, 2024
17
Suitable for metatranscriptomics?
#31 by ym2877 was closed Apr 10, 2024
3
virus masked human genome enhancement New feature or request
#30 by xiaoli-dong was closed Jan 29, 2024
5
Add versions and options to json log enhancement New feature or request
#29 by bede was closed Jan 13, 2024
1
Allow non-default databases in cloud bucket to be downloaded on first run enhancement New feature or request
#28 by bede was closed Jan 22, 2024 1.0.0
3
Regarding the choice of Reference genomes
#27 by LilyAnderssonLee was closed Aug 22, 2023
3
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