# example-snakemake

example snakemake workflow for workflow repository

~input.tsv~ may look like

```
sample	reference	fwd_pair	rev_pair
DRR198805_c1e4	ecoli.fasta	DRR198805_c1e4_R1_001.fastq.gz	DRR198805_c1e4_R2_001.fastq.gz
DRR198805_c1e4.2	ecoli.fasta	DRR198805_c1e4.2_R1_001.fastq.gz	DRR198805_c1e4.2_R2_001.fastq.gz
DRR198805_c2e4	ecoli.fasta	DRR198805_c2e4_R1_001.fastq.gz	DRR198805_c2e4_R2_001.fastq.gz
ERR4147226_c1e4	ecoli.fasta	ERR4147226_c1e4_R1_001.fastq.gz ERR4147226_c1e4_R2_001.fastq.gz
ERR4147226_c1e4.2	ecoli.fasta	ERR4147226_c1e4.2_R1_001.fastq.gz ERR4147226_c1e4.2_R2_001.fastq.gz
ERR4147226_c1e4.3	ecoli.fasta	ERR4147226_c1e4.3_R1_001.fastq.gz ERR4147226_c1e4.3_R2_001.fastq.gz
ERR4147226_c1e4.4	ecoli.fasta	ERR4147226_c1e4.4_R1_001.fastq.gz ERR4147226_c1e4.4_R2_001.fastq.gz
ERR4147226_c2e4	ecoli.fasta	ERR4147226_c2e4_R1_001.fastq.gz ERR4147226_c2e4_R2_001.fastq.gz
ERR4147226_c2e4.2	ecoli.fasta	ERR4147226_c2e4.2_R1_001.fastq.gz ERR4147226_c2e4.2_R2_001.fastq.gz
```