Issues
- 2
- 0
Automatically generate and cache minimap2 indexes to eliminate redundant indexing overhead
#39 opened by bede - 1
Mode: paired short read (Bowtie2) fails when index is provided as reference fasta file
#38 opened by Rohit-Satyam - 4
- 0
Allow remote index repository to be overridden
#37 opened by bede - 17
- 3
Suitable for metatranscriptomics?
#31 opened by ym2877 - 5
Incorporating Single-End Short Read Data Support
#34 opened by Ackia - 1
I think you can use --name (-n) on the mamba command line to override the environment name in the env file.
#33 opened by bdklahn - 4
virus masked human genome
#30 opened by xiaoli-dong - 2
BAM ingest
#1 opened by bede - 2
Running multiple hostile instances on same input file(s) corrupts decontamination statistics
#13 opened by bede - 1
Refactor with more OOP
#26 opened by bede - 3
- 5
Discard partially downloaded indexes
#20 opened by bede - 1
- 1
Add versions and options to json log
#29 opened by bede - 2
Crashes with exclusively contaminated input
#10 opened by bede - 3
- 3
- 3
- 1
- 1
Validate scrubbed output in tests/CI
#23 opened by bede - 1
Add completion message on stderr
#22 opened by bede - 1
Make --debug useful
#19 opened by bede - 10
Adding to Bioconda
#9 opened by rpetit3 - 6
Make fastq header stripping optional
#2 opened by bede - 0
Add aligner and index information to output json
#15 opened by bede - 0
Check if input files exist
#16 opened by bede - 0
- 0
- 0
Avoid overwriting output unless forced
#14 opened by bede - 1
Support for unpaired short reads
#5 opened by bede - 1
Support for stdin (and stdout)
#6 opened by bede - 1
Automatic masking
#12 opened by bede - 1
Support --custom-index
#8 opened by bede - 1
Support for uncompressed fastq
#7 opened by bede - 1
out_dir / --out-dir broken
#4 opened by bede - 1