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mhoban
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rainbow_bridge
GNU General Public License v3.0
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Typo in readme
#44
mhoban
closed
8 months ago
0
The --standalone-taxonomy run still requires you to specify your run type
#43
mhoban
closed
8 months ago
1
Investigate whether it's possible to show less-ugly results when there's an error
#42
mhoban
closed
3 weeks ago
1
Use awk instead of grep to remap sample IDs
#41
mhoban
closed
8 months ago
1
sample ids/file naming not fully interpreted for merging of paired end reads
#40
cajwalsh
closed
8 months ago
2
running insect after initial run through to LCA taxonomy does not use cached blast and lulu
#39
cajwalsh
closed
7 months ago
3
Percent identity default clarification
#38
vwishingrad
closed
10 months ago
0
BLAST step only using 10 cpus
#37
vwishingrad
closed
10 months ago
0
Change file extensions from ".tab" to ".tsv"
#36
vwishingrad
closed
7 months ago
4
Taxonomy file not using sample-map names
#35
vwishingrad
closed
8 months ago
5
Add DADA2 as a denoising option
#34
mhoban
opened
11 months ago
1
Nextflow fails at the dereplication stage when no primer matches are found by ngsfilter
#33
cajwalsh
closed
11 months ago
1
If --reads is not a directory, treat it as a glob
#32
mhoban
closed
6 months ago
1
Taxonomy scripts should include settings in output directory names
#31
mhoban
closed
11 months ago
1
runs with multiple barcode files are being processed incorrectly
#30
mhoban
closed
11 months ago
1
Allow pre-downloaded ranked lineage table
#29
mhoban
closed
11 months ago
1
Do sanity check for various reads options
#28
mhoban
closed
3 weeks ago
1
Confirm publishDir numbering for taxonomy step
#27
mhoban
closed
11 months ago
1
Allow taxonomy script to be run independently
#26
mhoban
closed
11 months ago
2
R taxonomy "dropped" vs. "", synthetic constructs
#25
cajwalsh
closed
3 weeks ago
6
If usearch is passed as an external executable, run it in its own process
#24
mhoban
closed
11 months ago
1
What if someone passes globs to --fwd and --rev?
#23
mhoban
closed
3 weeks ago
1
Improve error message when attempting to run eDNA flow on .gz files
#22
vwishingrad
closed
12 months ago
2
update the readme
#21
mhoban
closed
11 months ago
1
Not typing --base-dir before path to reads (when they are in a different directory) only runs get_lineage process
#20
cajwalsh
closed
12 months ago
2
Change name of filter_ambiguous_tags to filter_ambiguous_indices
#19
cajwalsh
closed
1 year ago
1
Fix support for old way of doing taxonomy assignment/collapse
#18
mhoban
closed
11 months ago
1
Make insect model download work the way it was going to work initially
#17
mhoban
closed
1 year ago
1
Fix profile configs
#16
mhoban
closed
2 months ago
2
Look into parallel blasting
#15
mhoban
opened
1 year ago
1
Allow user to specify file pattern using --reads for paired-end runs
#14
mhoban
closed
11 months ago
1
Figure out how to allocate cpus to lulu process
#13
mhoban
opened
1 year ago
0
Remove requirement for barcode file if doing --skip-demux
#12
mhoban
closed
1 year ago
1
Support gzipped reads
#11
mhoban
closed
12 months ago
1
Will usearch64 work the way it's entered?
#10
mhoban
closed
6 months ago
2
Enable customization of how sample IDs are interpreted from filenames
#9
mhoban
closed
12 months ago
2
Fix taxonomy assignment so it can use lulu OR regular output
#8
mhoban
closed
1 year ago
1
Detect whether there are multiple reads and suggest --illumina-demultiplexed option
#7
mhoban
closed
6 months ago
2
Improve input file handling
#6
mhoban
closed
3 weeks ago
1
Fix output filenames
#5
mhoban
closed
11 months ago
1
Add process statistics and settings files to process outputs
#4
mhoban
closed
7 months ago
1
Improve taxonomy python script
#3
mhoban
closed
11 months ago
4
Add phyloseq object creation
#2
mhoban
closed
11 months ago
1
Add WoRMS name validation
#1
mhoban
opened
1 year ago
0
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