Merge branch 'arc_to_v1.1' into 'main'

Arc to v1.1

See merge request brilator/samplearc_rnaseq!1

README.md

@@ -28,10 +28,9 @@ Directory | Purpose
 
 ### Adding large raw data via git lfs
 
-1. Before addind the files to the ARC, track them via `git lfs`
+1. Before adding the files to the ARC, track them via `git lfs`
 
     ```bash
-    git lfs track "*.fastq.gz"
     git lfs track "01_kallisto_index"    
     ```
 
@@ -40,9 +39,56 @@ Directory | Purpose
 1. Add them via `git add`
 
     ```bash
-    git add assays/Talinum_RNASeq_minimal/dataset/
-    git add runs/run1/01_kallisto_index
-    
+    git add runs/run1/01_kallisto_index    
     ```
 
 1. Commit
+
+
+
+## Bumping to ARC v1.1 (23.03.2022)
+
+### by arcCommander / shell
+> depends on arcCommander v3 or higher
+
+```bash
+arc a list
+
+arc study unregister -s TalinumFacultativeCAM # unregister old study version
+arc study add -s TalinumFacultativeCAM # add fresh
+mv TalinumFacultativeCAM.study.xlsx studies/TalinumFacultativeCAM/old.study.xlsx # move old study metadata to new study
+
+arc study add -s TalinumGenomeDraft # add draft genome as study
+mv externals/Talinum.gm.CDS.nt.fa studies/TalinumGenomeDraft/resources # mv genome to resources
+rm -r externals
+rm inv.json
+
+arc assay register -s TalinumFacultativeCAM -a Talinum_RNASeq_minimal # re-register assay 
+arc update
+
+mv assays/Talinum_RNASeq_minimal/protocols/01_plant_material.md studies/TalinumFacultativeCAM/protocols # move plant growth from assay to study
+
+arc assay remove -s TalinumFacultativeCAM -a RNASeq_Kallisto_quant # add computational parts as assay 
+
+```
+
+> note: soft assay 
+
+### by hand
+- move plant growth sheet isa.assay to isa.study
+- remove computational RNASeq sheet from assays as it partly duplicates the (not yet CWLed) kallisto workflow
+
+### add placeholder sample descriptors
+
+```bash
+arc_root=$(pwd)
+cd studies/TalinumFacultativeCAM/resources/
+touch \
+DB_097 \
+DB_099 \
+DB_103 \
+DB_161 \
+DB_163 \
+DB_165
+cd $arc_root
+```
\ No newline at end of file

externals/README.md → studies/TalinumGenomeDraft/README.md

@@ -2,5 +2,5 @@
 ### Talinum Genome ref
 File: Talinum.gm.CDS.nt.fa  
 Source: https://webdav.hhu.de/metdata/agweber/data/Eva_Maleckova-CAM/Genomics/Genome/Talinum-Flye-Polca_v201017/Talinum.gm.CDS.nt.fa  
-Contributor: Eva Maleckova - https://orcid.org/0000-0001-9062-3516  
+Contributor: Eva Maleckova - https://orcid.org/0000-0001-9062-3516