I was right, fixed the old --help mssg for read input format to match…

… the code and README!

README.md

@@ -213,13 +213,13 @@ By default, all possible comparisons are performed. Use `--deg` to change this.
 Specify your read files in `FASTQ` format with `--reads input.csv`. The file `input.csv` has to look like this for single-end reads:
 
 ```csv
-Sample,R,Condition,Source,Strandedness
-mock_rep1,/path/to/reads/mock1.fastq.gz,mock,,0
-mock_rep2,/path/to/reads/mock2.fastq.gz,mock,,0
-mock_rep3,/path/to/reads/mock3.fastq.gz,mock,,0
-treated_rep1,/path/to/reads/treat1.fastq.gz,treated,,0
-treated_rep2,/path/to/reads/treat2.fastq.gz,treated,,0
-treated_rep3,/path/to/reads/treat3.fastq.gz,treated,,0
+Sample,R1,R2,Condition,Source,Strandedness
+mock_rep1,/path/to/reads/mock1.fastq.gz,,mock,,0
+mock_rep2,/path/to/reads/mock2.fastq.gz,,mock,,0
+mock_rep3,/path/to/reads/mock3.fastq.gz,,mock,,0
+treated_rep1,/path/to/reads/treat1.fastq.gz,,treated,,0
+treated_rep2,/path/to/reads/treat2.fastq.gz,,treated,,0
+treated_rep3,/path/to/reads/treat3.fastq.gz,,treated,,0
 ```
 
 and for paired-end reads, like this:

main.nf

@@ -916,7 +916,7 @@ def helpMSG() {
     ${c_dim}Genomes and annotations from --autodownload, --genome and --annotation are concatenated.${c_reset}
 
     ${c_yellow}Input:${c_reset}
-    ${c_green}--reads${c_reset}                  A CSV file following the pattern: Sample,R,Condition,Source for single-end or Sample,R1,R2,Condition,Source for paired-end
+    ${c_green}--reads${c_reset}                  A CSV file following the pattern: Sample,R1,R2,Condition,Source,Strandedness (for single-end leave 'R2' column empty)
                                         ${c_dim}(check terminal output if correctly assigned)
                                         Per default, all possible comparisons of conditions in one direction are made. Use --deg to change.${c_reset}
     ${c_green}--autodownload${c_reset}           Specifies the species identifier for automated download [default: $params.autodownload]