mhoban rainbow_bridge issues

mhoban / rainbow_bridge

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Make some --skip-* options into things that are off by default

#94 mhoban opened 1 week ago
0
Improve parallelism of `unzip` process

#93 mhoban closed 1 week ago
1
Allow other filename extensions that just .fastq

#92 mhoban opened 2 weeks ago
0
BLAST db wildcard picks up too many files

#91 mhoban closed 2 weeks ago
1
If usearch executable is supplied, process should execute in system context

#90 mhoban closed 2 weeks ago
3
Streamline process execution for optimal parallelism

#89 mhoban closed 2 weeks ago
2
Unify taxonomy archive types

#88 mhoban opened 2 weeks ago
1
Make sure processes actually just use the cpus they're allocated

#87 mhoban closed 2 weeks ago
1
make generic get_web process to download things

#86 mhoban closed 3 weeks ago
1
zotu fasta and insect contain more zotus than zotu table

#85 cajwalsh opened 3 weeks ago
2
Make `collapse_taxonomy.R` choose the best sequence match when there are multiples

#84 mhoban closed 3 weeks ago
0
Add taxid of last non-"dropped" taxon to collapsed taxonomy

#83 mhoban opened 3 weeks ago
3
Support combined demultiplexing strategy

#82 mhoban closed 2 weeks ago
5
Feature Request: Employ Standard Unix Input Convention for `--reads`

#81 cbird808 closed 1 week ago
8
collapse_taxonomy incorrectly joins in the `last_taxon` value

#80 mhoban closed 3 weeks ago
1
uncultured, seqids in lca/collapse_taxonomy (many fewer zOTUs/taxa kept in lca results in more recent runs)

#79 cajwalsh closed 3 weeks ago
8
Add option to cleanup intermediate files to reduce storage

#78 mhoban opened 1 month ago
0
Add support for `--qualitymax` option in AdapterRemoval

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

#76 mhoban opened 1 month ago
0
write blast results to stdout

#75 ebfreel closed 2 weeks ago
2
Add more blast options

#74 mhoban opened 1 month ago
2
derep_vsearch zOTUs appearing in fasta but not zotu_table

#73 cajwalsh opened 1 month ago
0
lulu probably not behaving properly since major updates between 12/23 and 3/24

#72 cajwalsh opened 1 month ago
2
Rename fastqc output directories

#71 mhoban closed 1 month ago
0
added --skip-primer-match functionality to skip ngsfilter step

#70 cajwalsh closed 1 month ago
2
--standalone-taxonomy behavior with --zotu-table, finalize, and --insect

#69 cajwalsh opened 2 months ago
0
option to skip primer mismatch filter in ngsfilter command/process

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

#67 mhoban opened 3 months ago
1
Save settings in yaml/json format

#66 mhoban opened 3 months ago
2
Make taxonomy output directories like blast ones

#65 mhoban closed 3 months ago
0
Allow multiple taxonomic assignments (LCA or insect)?

#64 mhoban opened 4 months ago
0
Investigate results of blast searches against multiple databases

#63 mhoban closed 4 months ago
3
Add ability to make custom blast db

#62 mhoban opened 5 months ago
0
Put headers in blast results

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

#60 mhoban closed 5 months ago
1
Finalize process fails if neither lca nor insect are run

#59 mhoban closed 4 months ago
1
Save NCBI taxonomy dump

#58 mhoban closed 5 months ago
0
Redo blast options

#57 mhoban closed 5 months ago
3
Use dynamic containers?

#56 mhoban opened 5 months ago
0
Make vsearch default

#55 mhoban closed 5 months ago
1
Re-do the test data

#54 mhoban closed 4 months ago
2
Detect potentially-problematic .gz extension in sample map

#53 mhoban closed 2 weeks ago
1
Make column names better

#52 mhoban closed 7 months ago
1
Combine separate (LULU- and non-) taxonomy collapse processes

#51 mhoban closed 5 months ago
2
Consolidate singularity images for R

#50 mhoban closed 7 months ago
1
taxonomy qcov 100 may not (or not always) be returning qcov 100

#49 cajwalsh opened 7 months ago
0
Insect model name may not actually be case-insensitive

#48 mhoban closed 7 months ago
1
Code for external usearch executable probably won't work

#47 mhoban closed 2 weeks ago
1
Provide OTU table merged with insect taxonomy

#46 mhoban closed 7 months ago
2
Process/output folder numbering

#45 mhoban closed 7 months ago
3