Updates to documentation for readability

CHANGELOG.md

@@ -8,6 +8,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - Added the ability to include a `sample_name` column in the input samplesheet.csv. Allows for compatibility with IRIDA-Next input configuration [PR24](https://github.com/phac-nml/speciesabundance/pull/24)
+  - `sample_name` special characters will be replaced with `"_"`
+  - If no `sample_name` is supplied in the column sample will be used
+  - To avoid repeat values for `sample_name` all `sample_name` values will be suffixed with the unique `sample` value from the input file
 
 ## 2.1.1 - 2024/05/02
 

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 |
 
-A minimal [example samplesheet](../assets/samplesheet_minimal.csv) has been provided with the pipeline.
+An [example samplesheet](../assets/samplesheet.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/).
 
@@ -32,7 +32,7 @@ The sample sheet, when including the optional `sample_name` column, should look
 | ------- | ----------- | --------------- | --------------- |
 | SampleA | A1          | file_1.fastq.gz | file_2.fastq.gz |
 
-An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline, which includes the `sample_name` column.
+An [example samplesheet](../tests/data/samplename_samplesheet.csv) has been provided with the pipeline, which includes the `sample_name` column.
 
 # Parameters
 

assets/samplesheet.csv

@@ -1,4 +1,4 @@
-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,
+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 minimal [example samplesheet](../assets/samplesheet_minimal.csv) has been provided with the pipeline.
+A [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
 ### IRIDA-Next Optional Samplesheet Configuration
 
@@ -48,7 +48,7 @@ SAMPLE3,C3,sample3_R1.fastq.gz,
 | `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". |
 
-An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline, which includes the `sample_name` column.
+An [example samplesheet](../tests/data/samplename_samplesheet.csv) has been provided with the pipeline, which includes the `sample_name` column.
 
 ## Running the pipeline