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540 Commits

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Author SHA1 Message Date
Godwin N. Ani
fb5353fe96
Blacklist_and_greylist 2025-07-17 11:31:09 -04:00
Godwin N. Ani
4e63a165b7
Update contamination.py v1.0 2025-07-09 13:59:38 -04:00
Godwin N. Ani
99647c87bc
Update contamination.py 2025-07-09 13:59:28 -04:00
Adri K. Grow
586a9e0c63
Update CladeGrabbing.py 2025-07-08 07:54:58 -04:00
Katzlab
aec7f6caf9
Update ColorByClade.py 
Changed to root on bacteria (Ba) and not prokaryotes (Ba, Za).... did not test
 2025-07-01 16:18:54 -04:00
Godwin N. Ani
5486c4289b
Add files via upload 2025-07-01 11:11:21 -04:00
Adri K. Grow
c079b58d87
Update wrapper_submit.sh 2025-06-27 13:33:22 -04:00
Adri K. Grow
d16560f747
Update wrapper_submit.sh 2025-06-27 13:29:37 -04:00
Adri K. Grow
0b1feed651
Update ProcessAndRenameAssembledData.py 2025-06-27 12:39:05 -04:00
Adri K. Grow
d33ac6c2c3
Update Trim_Reads.py 2025-06-26 15:55:15 -04:00
Katzlab
ef6b633de7
Update guidance.py 
tidying comments
 2025-06-18 08:43:19 -04:00
Katzlab
c891188eec
Update guidance.py 
updated comments only to clarify versions
 2025-06-18 08:37:19 -04:00
Adri K. Grow
c767bd9a0a
Update Trim_Reads.py 2025-06-16 11:25:08 -04:00
Adri K. Grow
c84f3387ff
Update Trim_Reads.py 2025-06-13 12:41:35 -04:00
Adri K. Grow
3e4f4987a2
Update Trim_Reads.py 2025-06-13 12:41:17 -04:00
Katzlab
e7facbf6e7
Update PlotComps.r 
Fixed typo by changing

geom_line(data = enc_null, aes(GC3, ENc))

to 

geom_line(data = enc_null, aes(GC3S, ENc))
 2025-06-12 04:27:20 -04:00
Katzlab
3fe4ee3ae5
Update CUB.py 
Updates to notes only, including clarifying that we use GC3 and GC3S interchangeably .. though GC3S probably most correct
 2025-06-12 04:25:47 -04:00
Adri K. Grow
d81926f179
Update wrapper_submit.sh 2025-06-12 00:44:27 -04:00
Adri K. Grow
6cb8a7b98a
Update wrapper_submit.sh 2025-06-11 23:46:58 -04:00
GiuliaRibeiro
fdf525d433
Add files via upload 2025-06-11 10:17:50 -04:00
Katzlab
8ccde9800a
Update wrapper_submit.sh 
fixed typo to add backslash at end here
 2025-06-02 16:36:02 -04:00
Adri K. Grow
d32fbcc4e8
Update guidance.py 
Updated guidance command for local HPC users
 2025-06-02 11:23:34 -04:00
GiuliaRibeiro
9e4d605bff
Update trees.py 2025-04-18 13:01:33 -04:00
Auden Cote-L'Heureux
d01086e017
Update headers 2025-04-18 09:09:24 -04:00
Auden Cote-L'Heureux
e0930c5748
Update header for new guidance version 2025-04-18 09:09:03 -04:00
Auden Cote-L'Heureux
cc7a66b179
Update README.md to make links more clear 2025-04-18 08:57:06 -04:00
Auden Cote-L'Heureux
16a96f137e
Update guidance_path param 2025-04-18 08:48:42 -04:00
Auden Cote-L'Heureux
fa1f50e6f0
Update guidance_path param 2025-04-18 08:45:40 -04:00
Auden Cote-L'Heureux
9239110401
Updating guidance_path param 2025-04-18 08:45:23 -04:00
Auden Cote-L'Heureux
dc813c351a
Update utils.py 2025-04-18 08:44:21 -04:00
Auden Cote-L'Heureux
e452ae0117
Making the --concat_target_taxa argument optional 2025-04-15 16:23:19 -04:00
Godwin N. Ani
2651fe7b89
Update utils.py 2025-04-07 14:56:38 -04:00
Godwin N. Ani
c92f490837
Update contamination.py 2025-04-07 12:36:17 -04:00
Godwin N. Ani
7074a1e71a
Update contamination.py 2025-04-07 12:24:56 -04:00
Godwin N. Ani
95b26b1880
Update contamination.py 2025-04-07 12:20:56 -04:00
Godwin N. Ani
fba84adb17
Update contamination.py 2025-04-07 11:54:36 -04:00
Godwin N. Ani
8c7a1a2eed
Update contamination.py 2025-04-07 11:29:15 -04:00
Godwin N. Ani
e8aa277e44
Update contamination.py 2025-04-07 11:20:34 -04:00
Godwin N. Ani
998ce5bd9c
Update contamination.py 2025-04-07 11:06:32 -04:00
Adri K. Grow
4da74765ee
Add files via upload 2025-04-06 23:36:01 -04:00
Adri K. Grow
6a9ae23e8c
Delete Utilities/for_fastas/Cluster.py 2025-04-06 23:35:47 -04:00
Godwin N. Ani
0cfea8840c
Update contamination.py 2025-04-04 15:28:08 -04:00
Auden Cote-L'Heureux
d161957d86
Taking out 'both' option of contamination loop 2025-03-28 15:40:58 -04:00
Godwin N. Ani
4e52430af7
Update guidance.py 2025-03-25 12:35:43 -04:00
Godwin N. Ani
fdea233780
Update guidance.py 2025-03-25 12:16:02 -04:00
Godwin N. Ani
d7577022c4
Update CladeSizes.py 2025-03-24 15:01:48 -04:00
Godwin N. Ani
cf0948023d
Update guidance.py 2025-03-24 10:17:36 -04:00
Godwin N. Ani
04c41a6f44
Update guidance.py 2025-03-24 10:16:53 -04:00
Godwin N. Ani
c39df0e39d
Update utils.py 2025-03-24 10:11:35 -04:00
Godwin N. Ani
9b6b28ac03
Update Cluster.py 2025-03-21 13:48:23 -04:00