Add orthogroups data, update gitignore

.gitignore

@@ -1,15 +1,36 @@
-# Ignore any folder named 'archive' anywhere
+
+
+# ==================
+# System & Temporary
+# ==================
+
+# Any folder named 'archive' anywhere
 **/archive/
 
 # Ignore all .DS_Store files
 .DS_Store
 
-# Ignore SIRIUS project file
+
+# ==========
+# LC-MS Data
+# ==========
+
+# SIRIUS project file
 lcms/sirius/pipernet.sirius
 
-# Ignore everything inside rnaseq except assemblies folder
+# LC-MS data preparation outputs
+lcms/ftable_clean.csv
+lcms/ntable_clean.csv
+
+
+# ============
+# RNA-Seq Data
+# ============
+
+# Everything inside rnaseq except assemblies folder
 rnaseq/*
 !rnaseq/assemblies/
+!rnaseq/orthogroups/
 
 # Inside assemblies, ignore all subfolders' contents except explicitly allowed files
 rnaseq/assemblies/*/*

rnaseq/orthogroups/sonicparanoid/graph_only/ortholog_groups.tsv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e2922ae899a3d2e25a6f40aeca486fad8d1835ca3b48dbee49e1b4ccc55c11a5
+size 25439824

rnaseq/orthogroups/sonicparanoid/graph_only/run_info.txt

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+Date:	Fri Jul 12 11:02:55 2024
+SonicParanoid 2.0.4
+Run ID:	piperNET
+Input directory:	/home2/titodamiani/PiperNET/results/orthogroups/proteomes
+Main output directory:	/home2/titodamiani/PiperNET/results/orthogroups/output_v204
+Run directory:	/home2/titodamiani/PiperNET/results/orthogroups/output_v204/runs/piperNET
+Input proteomes:	13
+Run mode:	default
+Alignment tool:	diamond
+Diamond sensitivity:	very-sensitive
+Threads:	8
+Minimum bitscore:	40
+Max length difference for in-paralogs:	0.75
+Ortholog tables-merging threshold:	0.75
+MCL inflation:	1.5
+Sequence DB directory:	/home2/titodamiani/PiperNET/results/orthogroups/output_v204/seqs_dbs/
+Alignment directory:	/home2/titodamiani/PiperNET/results/orthogroups/output_v204/alignments/
+Pairwise tables DB directory:	/home2/titodamiani/PiperNET/results/orthogroups/output_v204/orthologs_db
+Directory with pairwise orthologs:	/home2/titodamiani/PiperNET/results/orthogroups/output_v204/runs/piperNET/pairwise_orthologs/
+Directory with ortholog groups:	/home2/titodamiani/PiperNET/results/orthogroups/output_v204/runs/piperNET/ortholog_groups/
+Memory per threads (Gigabytes):	11.64
+Minimum memory per threads (Gigabytes):	1.0
+Perfom only graph-based orthology:	True
+Update run:	False
+Create query database indexes:	False
+Complete alignments:	False
+Overwrite pair-wise ortholog tables:	False
+Complete overwrite:	False
+Skip creation of ortholog groups:	False
+Compress alignments:	True
+Compression level:	5
+SonicParanoid installation:	/home2/titodamiani/conda-envs/sonicparanoid/lib/python3.9/site-packages/sonicparanoid
+Installation type:	Python
+Python version:	3.9.19 | packaged by conda-forge | (main, Mar 20 2024, 12:50:21) 
+[GCC 12.3.0]
+Python executables:	/home2/titodamiani/conda-envs/sonicparanoid/bin/python3.9