The design file has to be a csv (not tsv).
The file must contain a column named sample which associates a name of your choice to each sample.
The file must also contain the location of the fastq file for each sample.
These columns must be named file for a single-end experiment, and file1 and file2 for a paired-end experiment.
All the other columns contain the different conditions of the experiment (treatment, time...).
For example, the design file for the single end test data contains:
sample,file,treatment
control1,fastq/single_end/sample1.fastq.gz,untreated
control2,fastq/single_end/sample2.fastq.gz,untreated
treatment2,fastq/single_end/sample5.fastq.gz,treated
And the one for the paired end test data contains:
sample,file1,file2,treatment
control2,fastq/paired_end/sample2_r1.fastq.gz,fastq/paired_end/sample2_r2.fastq.gz,untreated
control3,fastq/paired_end/sample3_r1.fastq.gz,fastq/paired_end/sample3_r2.fastq.gz,untreated
treatment3,fastq/paired_end/sample6_r1.fastq.gz,fastq/paired_end/sample6_r2.fastq.gz,treated
You can now configure the pipeline.