Defining your samples in the sample list
The workflow requires you to supply a file with some information on your samples. The path to this file is specified with the sample_list: parameter in the configuration file.
As a minimum the file must contain the columns sample, unit and fq1. Paired-end samples also require the fq2 column for the mate 2 read file.
A very basic sample file may look like this:
| sample | unit | fq1 | fq2 |
|---|---|---|---|
| sample1 | 1 | examples/data/sample1_1_R1.fastq.gz | examples/data/sample1_1_R2.fastq.gz |
| sample2 | 1 | examples/data/sample2_11_R1.fastq.gz | examples/data/sample2_11_R2.fastq.gz |
| sample3 | 1 | examples/data/sample3_21_R1.fastq.gz |
The columns fq1 and fq2 (for paired-end data) specify the paths to fastq files which will be used as input to the workflow.
Specifying assemblies
You may also include a column named assembly with names for assemblies to create. The assembly field can be comma-separated entries specifying several assemblies per sample/unit combination.
For instance, with a sample file like this:
| sample | unit | assembly | fq1 | fq2 |
|---|---|---|---|---|
| sample1 | 1 | sample1,all | examples/data/sample1_1_R1.fastq.gz | examples/data/sample1_1_R2.fastq.gz |
| sample2 | 1 | sample2,all | examples/data/sample2_11_R1.fastq.gz | examples/data/sample2_11_R2.fastq.gz |
| sample3 | 1 | sample3,all | examples/data/sample3_21_R1.fastq.gz |
a total of 4 assemblies will be generated:
-
sample1,sample2andsample3with input only from each sample respectively, and -
allwith input from all samples
