fix: mv configuration docs to specific README file

README.md

@@ -2,7 +2,7 @@
 
 ## Overview
 
-This is a Snakemake pipeline for the integrated analysis of single copy genes, transposable elements and tRNAs. It performs standard quality control checks and genome alignment in three different ways specialized either for single copy genes or transposable elements. It then quantifies gene expression depending on how the alignement step was performed. Finally it performs differential gene expression analysis yielding lists of genes significantly deregulated between two given conditions.
+This is a Snakemake workflow for the integrated analysis of single copy genes, transposable elements and tRNAs. It performs standard quality control checks and genome alignment in three different ways specialized either for single copy genes or transposable elements. It then quantifies gene expression depending on how the alignement step was performed. Finally it performs differential gene expression analysis yielding lists of genes significantly deregulated between two given conditions.
 
 ![Overall 3t-seq workflow](docs/figures/3t-wf.png)
 
@@ -47,92 +47,8 @@ After the pipeline completes, you can find the results in the `results/` directo
 
 ## Configuration
 
-Adjust parameters in the `config.yaml` file to match your experimental setup.
-
-Here is an example config file:
-
-```yaml
-# config/config.yaml
-
-# A list of datasets 
-sequencing_libraries:
-  - name: GSE13073
-    sample_sheet: sample-sheet.csv
-    trimmomatic: >-
-      "ILLUMINACLIP:TruSeq3-PE.fa:1:0:15:2
-       SLIDINGWINDOW:20:22
-       MAXINFO:20:0.6
-       LEADING:22
-       TRAILING:20
-       MINLEN:75"
-    star: >-
-      "--seedSearchStartLmax 30
-       --outFilterMismatchNoverReadLmax 0.04
-       --winAnchorMultimapNmax 40"
-    bamCoverage: "--binSize 50 --normalizeUsing None"
-
-#   - name: ...
-#     sample_sheet: ...
-#     trimmomatic: ...
-#     star: ...
-#     bamCoverage: ...
-
-# 
-globals:
-  # path to reads folder 
-  # NB: ./GSE13073 is expected to exist
-  reads_folder: .
-
-  # path to results folder
-  results_folder: results/
-
-  # path to qc
-  qc_folder: results/qc
-
-  # path to log
-  log_folder: results/log
-
-  # path to references
-  references_folder: results/references
-
-  # temp folder
-  tmp_folder: /tmp
-
-  # path to analysis
-  analysis_folder: results/analysis
-
-# genome informations
-genome:
-  # genome label
-  label: mm10
-
-  # annotation type
-  # can be ensembl, mgi, gencode
-  annotation_type: ensembl
-
-  # URL or path to genome sequence
-  fasta_url: <Genome fasta URL>
-
-  # URL or path to genome annotation file
-  gtf_url: <Genome annotation URL>
-
-  # URL to gtRNAdb zip file
-  gtrnadb_url: <GtRNADb bundle URL>
-
-# Differential expression analysis parameters
-deseq2:
-  # wd
-  working_directory: ../../..  
-
-  # DESeq2 test name, can be Wald or LRT
-  test: Wald
-
-  # name of the column from sample sheet with experimental variable
-  variable: genotype
-
-  # base level from variable column
-  reference_level: wt
-```
+Adjust parameters in the `config.yaml` file to match your experimental setup. See `config/README.md` for further instructions.
+
 
 ### Sample sheet preparation