mhoban rainbow_bridge issues

mhoban / rainbow_bridge

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investigate obitools4

#127 mhoban opened 2 weeks ago
0
Issues with degenerate bases in primers

#126 ericgarciaresearch opened 2 weeks ago
2
Update phyloseq generation process

#125 mhoban closed 4 weeks ago
0
Fix phyloseq output

#124 mhoban closed 4 weeks ago
0
Fix caching/resumption problems and issues related to running insect without blast

#123 mhoban closed 1 month ago
0
Trying to run insect without blast throws error

#122 mhoban closed 1 month ago
0
Possible variable scoping issues, use `def` keyword for variable declaration

#121 mhoban closed 1 month ago
0
Re-running finished pipeline with `--insect` causes blast to run again

#120 mhoban closed 1 month ago
1
Bullet Proofing LCA `nodes_dmp` `taxid_lineage_dump`

#119 cbird808 closed 1 month ago
3
Allow standalone taxonomic assignment via insect

#118 mhoban opened 1 month ago
0
Pull extra BLAST options out of input channel.

#117 mhoban closed 1 month ago
0
Implement unit testing / continuous integration

#116 mhoban opened 1 month ago
0
`blast` task doesn't need extra options as input channel

#115 mhoban closed 1 month ago
0
Update standalone taxonomy and fix some lca code internals

#114 mhoban closed 1 month ago
0
Separate outputs of `lca` process

#113 mhoban closed 1 month ago
0
Add `--zotu-identity` parameter for zOTU table generation step

#112 mhoban closed 1 month ago
1
Make the various "no file" placeholders consistent

#111 mhoban closed 1 month ago
0
Allow custom taxonomic lineages to match custom BLAST dastabases

#110 mhoban closed 1 month ago
0
Standalone taxonomy process shouldn't merge zotu table

#109 mhoban closed 1 month ago
1
Add e-value as threshold option for `collapse_taxonomy`

#108 mhoban opened 1 month ago
0
Restructure some processes

#107 mhoban opened 1 month ago
0
collapse-taxonomy not working with pid = 100, diff = 0

#106 cajwalsh closed 1 month ago
7
Add average percent ID match to LCA table

#105 mhoban opened 1 month ago
1
fwd/rev reads need to be reordered after unzip

#104 mhoban closed 1 month ago
3
Allow `--mate-separator` option for AdapterRemoval

#103 mhoban closed 1 month ago
1
Allow custom taxdb for custom blast databases

#102 mhoban closed 1 month ago
4
Add option to save sequence attributes in tabular files

#101 mhoban closed 1 month ago
1
Allow lists of reads in file?

#100 mhoban opened 1 month ago
1
`filter_uncultured` in `collapse_taxonomy.R`

#99 cbird808 closed 1 month ago
3
`qcov` filter in `collapse_taxonomy.R` virtually negates the function of `diff_thresh`

#98 cbird808 closed 1 month ago
2
Overly stringent filtering in `collapse_taxonomy.R`

#97 cbird808 closed 1 month ago
5
Rather than dummy filenames, can we set options to `false`?

#96 mhoban closed 1 month ago
1
Finalize fails if you don't do `insect` or `collapse-taxonomy`

#95 mhoban closed 2 months ago
2
Make some --skip-* options into things that are off by default

#94 mhoban closed 2 months ago
1
Improve parallelism of `unzip` process

#93 mhoban closed 2 months ago
1
Allow other filename extensions that just .fastq

#92 mhoban closed 1 month ago
1
BLAST db wildcard picks up too many files

#91 mhoban closed 3 months ago
1
If usearch executable is supplied, process should execute in system context

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

#89 mhoban closed 3 months ago
2
Unify taxonomy archive types

#88 mhoban opened 3 months ago
1
Make sure processes actually just use the cpus they're allocated

#87 mhoban closed 3 months ago
1
make generic get_web process to download things

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

#85 cajwalsh closed 1 month ago
17
Make `collapse_taxonomy.R` choose the best sequence match when there are multiples

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

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

#82 mhoban closed 3 months ago
5
Feature Request: Employ Standard Unix Input Convention for `--reads`

#81 cbird808 closed 2 months ago
8
collapse_taxonomy incorrectly joins in the `last_taxon` value

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

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

#78 mhoban opened 3 months ago
0