visualize example run dir corresponsing to samplesheet

Author: kedhammar

docs/usage.md

@@ -10,35 +10,45 @@
 
 ## Samplesheet input
 
-You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
+You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location.
 
 ```bash
 --input '[path to samplesheet file]'
 ```
 
 ### Full samplesheet
 
+The following simple run dir structure...
+
+```
+run_dir
+├── sample1_lane1_group1_r1.fq.gz
+├── sample2_lane1_group1_r1.fq.gz
+├── sample3_lane2_group2_r1.fq.gz
+└── sample4_lane2_group3_r1.fq.gz
+```
+
+...would be represented in the following samplesheet (shown as .tsv for readability)
+
 ```csv title="samplesheet.csv"
-sample,lane,group,fastq_1,fastq_2,rundir
-CONTROL_REP1,1,,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
-CONTROL_REP2,1,,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
-CONTROL_REP3,1,,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
-TREATMENT_REP1,2,GROUP1,AEG588A4_S4_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
-TREATMENT_REP2,2,GROUP1,AEG588A5_S5_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
-TREATMENT_REP3,2,GROUP2,AEG588A6_S6_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
-TREATMENT_REP3,2,GROUP2,AEG588A6_S6_L004_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
+sample  lane  group   fastq_1                                       fastq_2 rundir
+sample1 1     group1  path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir
+sample2 1     group1  path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir
+sample3 2     group2  path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir
+sample4 2     group3  path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir
+
 ```
 
 | Column    | Description                                                                                                                                                                            |
 | --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
 | `lane`    | Lane where the sample was processed on an Illumina instrument (optional).                                                                                                              |
 | `group`   | Group the sample belongs too, useful when several groups are pooled together (optional).                                                                                               |
-| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
+| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
 
-An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
+Another [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
 ## Running the pipeline