Base Folder Structure

base folder parameter from your config.yaml file defines the folder which will be used to store all the output files generated from this pipeline. When you run pipeline with tasks:0 (i.e. full analysis), you will get following folder tree as a output. Let us assume following is samples.csv file

run,is_paired
SRR0000001,true
SRR0000002,false

After running snakemake in the pipeline folder with default options, you will get following folder structure.

base
├── sra
│   ├── SRR0000001.sra
│   └── SRR0000002.sra
├── fastq
│   ├── SRR0000001.sra_1.fastq
│   ├── SRR0000001.sra_2.fastq
|   └── SRR0000002.sra.fastq
├── filtered
│   ├── SRR0000001.sra.filtered_1.fastq
│   ├── SRR0000001.sra.filtered_2.fastq
|   └── SRR0000002.sra.filtered.fastq
├── bams
│   ├── SRR0000001.sra.Aligned.sortedByCoord.out.bam + other log files
|   └── SRR0000002.sra.Aligned.sortedByCoord.out.bam + other log files
├── index
│   ├── star
|   |   └── SAindex + other files
|   ├── sortmerna
|   |   └── idx + other folders
|   |       └── *.stats, *.dat + other files 
|   ├── salmon
|   |   └── pos.bin + other files
|   └── kallisto / ..
├── mappings
|   ├── stringtie
|   |   ├── SRR0000001
|   |   |   └── SRR0000001_gene_expression.tsv + other files
|   |   └── SRR0000002 / .. 
|   ├── salmon
|   |   ├── SRR0000001
|   |   |   └── quant.sf + other files and folders
|   |   └── SRR0000002 / .. 
|   └── kallisto
|       ├── SRR0000001 
|       |   └── abundance.tsv + other files
|       └── SRR0000002 / .. 
├── deseq2
|   ├── counts
|   |   ├── SRR0000001
|   |   |   |── SRR0000001.star.counts
|   |   |   |── SRR0000001.star.counts.stat
|   |   |   ├── SRR0000001.stringtie.counts
|   |   |   ├── SRR0000001.stringtie_transcripts.counts
|   |   |   ├── SRR0000001.salmon.counts
|   |   |   └── SRR0000001.kallisto.counts
|   |   └── SRR0000002 / ..
|   └── analysis
|       ├── star
|       |    ├── combined.counts
|       |    ├── analysis.log
|       |    └── DESeq2 analysis files and their combinations
|       ├── salmon/...
|       ├── stringtie/..
|       └── kallisto/..
├── quality_report.html
├── quality_report_data/..
└── logs

Note: Above tree diagram is only for illustrative purposes, there might be more or less files based on your system and workflow.