mhoban rainbow_bridge issues

mhoban / rainbow_bridge

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Add support for `--qualitymax` option in AdapterRemoval

#77 mhoban closed 3 months ago
1
Fix ambiguous bases in barcodes file

#76 mhoban opened 3 months ago
0
write blast results to stdout

#75 ebfreel closed 3 months ago
2
Add more blast options

#74 mhoban closed 1 month ago
3
derep_vsearch zOTUs appearing in fasta but not zotu_table

#73 cajwalsh closed 1 month ago
1
lulu probably not behaving properly since major updates between 12/23 and 3/24

#72 cajwalsh opened 4 months ago
5
Rename fastqc output directories

#71 mhoban closed 4 months ago
0
added --skip-primer-match functionality to skip ngsfilter step

#70 cajwalsh closed 4 months ago
2
--standalone-taxonomy behavior with --zotu-table, finalize, and --insect

#69 cajwalsh opened 4 months ago
1
option to skip primer mismatch filter in ngsfilter command/process

#68 cajwalsh closed 4 months ago
1
Add option to save current configuration as params file

#67 mhoban opened 5 months ago
1
Save settings in yaml/json format

#66 mhoban opened 5 months ago
3
Make taxonomy output directories like blast ones

#65 mhoban closed 5 months ago
0
Allow multiple taxonomic assignments (LCA or insect)?

#64 mhoban closed 1 month ago
0
Investigate results of blast searches against multiple databases

#63 mhoban closed 6 months ago
3
Add ability to make custom blast db

#62 mhoban closed 1 month ago
0
Put headers in blast results

#61 mhoban closed 3 months ago
2
Allow the ability to blast against custom db but NOT ncbi

#60 mhoban closed 8 months ago
1
Finalize process fails if neither lca nor insect are run

#59 mhoban closed 6 months ago
1
Save NCBI taxonomy dump

#58 mhoban closed 8 months ago
0
Redo blast options

#57 mhoban closed 8 months ago
3
Use dynamic containers?

#56 mhoban closed 1 month ago
1
Make vsearch default

#55 mhoban closed 8 months ago
1
Re-do the test data

#54 mhoban closed 6 months ago
2
Detect potentially-problematic .gz extension in sample map

#53 mhoban closed 3 months ago
1
Make column names better

#52 mhoban closed 9 months ago
1
Combine separate (LULU- and non-) taxonomy collapse processes

#51 mhoban closed 8 months ago
2
Consolidate singularity images for R

#50 mhoban closed 9 months ago
1
taxonomy qcov 100 may not (or not always) be returning qcov 100

#49 cajwalsh opened 10 months ago
0
Insect model name may not actually be case-insensitive

#48 mhoban closed 10 months ago
1
Code for external usearch executable probably won't work

#47 mhoban closed 3 months ago
1
Provide OTU table merged with insect taxonomy

#46 mhoban closed 10 months ago
2
Process/output folder numbering

#45 mhoban closed 10 months ago
3
Typo in readme

#44 mhoban closed 10 months ago
0
The --standalone-taxonomy run still requires you to specify your run type

#43 mhoban closed 10 months ago
1
Investigate whether it's possible to show less-ugly results when there's an error

#42 mhoban closed 3 months ago
1
Use awk instead of grep to remap sample IDs

#41 mhoban closed 10 months ago
1
sample ids/file naming not fully interpreted for merging of paired end reads

#40 cajwalsh closed 10 months ago
2
running insect after initial run through to LCA taxonomy does not use cached blast and lulu

#39 cajwalsh closed 9 months ago
3
Percent identity default clarification

#38 vwishingrad closed 1 year ago
0
BLAST step only using 10 cpus

#37 vwishingrad closed 1 year ago
0
Change file extensions from ".tab" to ".tsv"

#36 vwishingrad closed 10 months ago
4
Taxonomy file not using sample-map names

#35 vwishingrad closed 10 months ago
5
Add DADA2 as a denoising option

#34 mhoban opened 1 year ago
1
Nextflow fails at the dereplication stage when no primer matches are found by ngsfilter

#33 cajwalsh closed 1 year ago
1
If --reads is not a directory, treat it as a glob

#32 mhoban closed 8 months ago
1
Taxonomy scripts should include settings in output directory names

#31 mhoban closed 1 year ago
1
runs with multiple barcode files are being processed incorrectly

#30 mhoban closed 1 year ago
1
Allow pre-downloaded ranked lineage table

#29 mhoban closed 1 year ago
1
Do sanity check for various reads options

#28 mhoban closed 3 months ago
1

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