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Author	SHA1	Message	Date
Godwin N. Ani	c042f62249	Update wrapper_submit.sh	2025-08-25 10:59:29 -04:00
Godwin N. Ani	efebf01057	Update wrapper_submit.sh	2025-08-25 10:58:25 -04:00
Adri K. Grow	0fc18547d6	Update ReadMapping.py	2025-08-22 13:16:37 -04:00
Adri K. Grow	fee7125729	Update ProcessAndRenameAssembledData.py	2025-08-21 10:40:08 -04:00
Adri K. Grow	c92cfb1b19	Update ReadMapping.py ... Making things more universally applicable rather than keeping the hardcoded index range	2025-08-18 14:13:11 -04:00
Adri K. Grow	5fcd3b937e	Update CladeGrabbing.py	2025-08-18 10:56:17 -04:00
Adri K. Grow	20d3926f10	Update CladeGrabbing.py ... Adding new optional arguments to support two-step clade filtering within one run of the script.	2025-08-18 10:54:25 -04:00
GiuliaRibeiro	873862adbc	Update guidance.py ... fixed 70gapTrimmed line	2025-08-07 09:53:42 -04:00
Godwin N. Ani	333a7bc063	Update run_eukphylo.sh	2025-07-29 17:43:37 -04:00
Godwin N. Ani	b582321c3a	Update guidance.py	2025-07-17 14:47:39 -04:00
Godwin N. Ani	7a2320284a	Update utils.py	2025-07-17 14:46:52 -04:00
Godwin N. Ani	f53b6926c5	Add files via upload	2025-07-17 11:42:28 -04:00
Godwin N. Ani	399811662c	Delete PTL2/Black_and_Grey_list_GuidanceSisSubsisters_RemovedSeq_Conserved_PTLms_June2024_ML (1).txt	2025-07-17 11:42:19 -04:00
Godwin N. Ani	a05f94c9fa	Add files via upload	2025-07-17 11:41:09 -04:00
Godwin N. Ani	343496b598	Delete PTL2/Black_and_Grey_list_GuidanceSisSubsisters_RemovedSeq_Conserved_PTLms_June2024_ML.txt	2025-07-17 11:40:56 -04:00
Godwin N. Ani	3f9ef410a7	Rename Black_and_Grey_list_GuidanceSisSubsisters_RemovedSeq_Conserved_PTLms_June2024_ML (1).txt to Black_and_Grey_list_GuidanceSisSubsisters_RemovedSeq_Conserved_PTLms_June2024_ML.txt	2025-07-17 11:31:34 -04:00
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