Edits to README and usage docs

README.md

@@ -14,7 +14,7 @@ The input to the pipeline is a standard sample sheet (passed as `--input samples
 | ------- | --------------- | --------------- |
 | SampleA | file_1.fastq.gz | file_2.fastq.gz |
 
-An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
+An [example samplesheet](../assets/samplesheet_minimal.csv) has been provided with the pipeline.
 
 The structure of this file is defined in [assets/schema_input.json](assets/schema_input.json). Validation of the sample sheet is performed by [nf-validation](https://nextflow-io.github.io/nf-validation/).
 

assets/samplesheet.csv

@@ -1,4 +1,4 @@
-sample,fastq_1,fastq_2
-SAMPLE1,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R2.fastq.gz
-SAMPLE2,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R2.fastq.gz
-SAMPLE3,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz,
+sample,sample_name,fastq_1,fastq_2
+SAMPLE1,A1,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R2.fastq.gz
+SAMPLE2,B2,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R2.fastq.gz
+SAMPLE3,C3,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz,

assets/samplesheet_minimal.csv

@@ -0,0 +1,4 @@
+sample,fastq_1,fastq_2
+SAMPLE1,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R2.fastq.gz
+SAMPLE2,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R2.fastq.gz
+SAMPLE3,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz,

docs/usage.md

@@ -26,7 +26,7 @@ SAMPLE2,sample2_R1.fastq.gz,sample2_R2.fastq.gz
 SAMPLE3,sample3_R1.fastq.gz,
 ```
 
-A [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
+A [example samplesheet](../assets/samplesheet_minimal.csv) has been provided with the pipeline.
 
 ### IRIDA-Next Optional Samplesheet Configuration