Re-organize files to match new project structure

[lcolladotor]

Overall file structure ideas https://lcolladotor.github.io/bioc_team_ds/organizing-your-work.html

Live examples: https://github.com/LieberInstitute/Visium_IF_AD and the newer https://github.com/LieberInstitute/DLPFC_snRNAseq

See more on Slack at https://jhu-genomics.slack.com/archives/C01EA7VDJNT/p1630516674026100

Current status:

 $ ls -lh /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC
total 234K
drwxrws---  2 lcollado lieber_lcolladotor   31 Jul 28 10:47 analysis
drwxrws--- 14 lcollado lieber_lcolladotor   14 Nov 25  2020 FASTQ
drwxrws---  2 lcollado lieber_lcolladotor    2 Nov 18  2020 html
drwxrws---  8 lcollado lieber_lcolladotor    9 Jul 14 13:25 Images
drwxrws---  4 lcollado lieber_lcolladotor   16 Jul 23 16:53 images_raw_align_json
drwxrws---  4 lcollado lieber_lcolladotor    4 Feb 17  2021 outputs
drwxrws---  6 lcollado lieber_lcolladotor   35 Aug  3 09:08 plots
drwxrws---  3 lcollado lieber_lcolladotor    5 Mar 22 12:33 rdata
-rw-rw----  1 lcollado lieber_lcolladotor 1.8K Nov 18  2020 README.md
drwxrws---  2 lcollado lieber_lcolladotor    5 Jul 26 12:27 sample_info
drwxrws---  3 lcollado lieber_lcolladotor    3 Jul 26 11:01 scripts
-rw-rw----  1 lcollado lieber_lcolladotor  270 Feb 15  2021 spatialDLPFC.Rproj

More specifically:

• create raw-data, code, processed-data
• move analysis to code/
• move FASTQ to raw-data/
• delete html for now, can be remade under processed-data later, like in sub-directories as in https://github.com/LieberInstitute/DLPFC_snRNAseq/tree/main/processed-data/02_cellranger_metrics
• move Images to raw-data/
• move images_raw_align_json to raw-data/
• move rdata to processed-data, maybe even to sub-directories like https://github.com/LieberInstitute/DLPFC_snRNAseq/tree/main/processed-data/02_cellranger_metrics
• move sample_info to raw-data/
• move scripts to code/