phac-nml · sgsutcliffe · Sep 23, 2024 · Sep 16, 2024 · Sep 16, 2024 · Sep 16, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,18 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Development
+
+### `Changed`
+
+- Modified the template for input csv file to include a `sample_name` column in addition to `sample` in-line with changes to [IRIDA-Next update] as seen with the [speciesabundance pipeline]
+  - `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
+
+[IRIDA-Next update]: https://github.com/phac-nml/irida-next/pull/678
+[speciesabundance pipeline]: https://github.com/phac-nml/speciesabundance/pull/24
+
 ## [2.1.1] - 2024/08/21
 
 ### `Changed`

diff --git a/README.md b/README.md
@@ -8,19 +8,28 @@ This is the [nf-core](https://nf-co.re/)-based pipeline for [SNVPhyl](https://sn
 
 Input is provided to SNVPhyl in the form of a samplesheet (passed as `--input samplesheet.csv`). This samplesheet is a CSV-formated file, which may be provided as a URI (ex: a file path or web address), and has the following format:
 
-| sample  | fastq_1                    | fastq_2                    | reference_assembly           | metadata_1 | metadata_2 | metadata_3 | metadata_4 | metadata_5 | metadata_6 | metadata_7 | metadata_8 |
-| ------- | -------------------------- | -------------------------- | ---------------------------- | ---------- | ---------- | ---------- | ---------- | ---------- | ---------- | ---------- | ---------- |
-| SAMPLE1 | /path/to/sample1_fastq1.fq | /path/to/sample1_fastq2.fq | /path/to/sample1_assembly.fa | meta1      | meta2      | meta3      | meta4      | meta5      | meta6      | meta7      | meta8      |
-| SAMPLE2 | /path/to/sample2_fastq1.fq |                            |                              | meta1      | meta2      | meta3      | meta4      | meta5      | meta6      | meta7      | meta8      |
+| sample  | sample_name  | fastq_1                    | fastq_2                    | reference_assembly           | metadata_1 | metadata_2 | metadata_3 | metadata_4 | metadata_5 | metadata_6 | metadata_7 | metadata_8 |
+| ------- | ------------ | -------------------------- | -------------------------- | ---------------------------- | ---------- | ---------- | ---------- | ---------- | ---------- | ---------- | ---------- | ---------- |
+| SAMPLE1 | sample_name1 | /path/to/sample1_fastq1.fq | /path/to/sample1_fastq2.fq | /path/to/sample1_assembly.fa | meta1      | meta2      | meta3      | meta4      | meta5      | meta6      | meta7      | meta8      |
+| SAMPLE2 | sample_name2 | /path/to/sample2_fastq1.fq |                            |                              | meta1      | meta2      | meta3      | meta4      | meta5      | meta6      | meta7      | meta8      |
 
 The columns are defined as follows:
 
-- `sample`: The unique sample identifier to associate with the reads (and optionally the reference assembly).
+- `sample`: Mandatory unique sample identifier. The unique sample identifier to associate with the reads (and optionally the reference assembly).
+- `sample_name`: Optional, and overrides `sample` for outputs (filenames and sample names) and reference assembly identification.
 - `fastq_1`: A URI (ex: a file path or web address) to either single-end FASTQ-formatted reads or one pair of pair-end FASTQ-formatted reads.
 - `fastq_2`: (Optional) If `fastq_1` is paired-end, then this field is a URI to reads that are the other pair of reads associated with `fastq_1`.
 - `reference_assembly`: (Optional) A URI to a reference assembly associated with the sample, so that it may be referenced on the command line by the sample identifier for use as the reference for the whole pipeline. However, it may be easier to leave these fields blank and specify the reference using the `--refgenome` parameter.
 - `metadata_1...8`: (Optional) Permits up to 8 columns for user-defined contextual metadata associated with each `sample`. Refer to [Metadata](#metadata) for more information.
 
+### When to use `sample` vs `sample_name`
+
+Either can be used to identify the reference assembly with the parameter `--reference_sample_id`.
+
+`sample` is a unique identifier, designed to be used internally or in IRIDA-Next, or when `sample_name` is not provided.
+
+`sample_name`, allows more flexibility in naming output files or sample identification. Unlike `sample`, `sample_name` is not required to contain unique values. `Nextflow` requires unique sample names, and therefore in the instance of repeat `sample_names`, `sample` will be suffixed to any `sample_name`. Non-alphanumeric characters (excluding `_`,`-`,`.`) will be replaced with `"_"`.
+
 The structure of this file is defined in [assets/schema_input.json](assets/schema_input.json). Please see [assets/samplesheet.csv](assets/samplesheet.csv) to see an example of a samplesheet for this pipeline.
 
 # Parameters
@@ -45,7 +54,7 @@ The optional parameters are as follows:
 ### Reference
 
 - `--refgenome`: a URI to the reference genome to use during pipeline analysis
-- `--reference_sample_id`: the sample identifier of a sample in the samplesheet that contains a provided `reference_assembly` to use as a reference genome during pipeline analysis
+- `--reference_sample_id`: the sample identifier of a sample (`sample` or `sample_name`) in the samplesheet that contains a provided `reference_assembly` to use as a reference genome during pipeline analysis
 
 Please use only one of `--refgenome` or `--reference_sample_id` and not both.
 

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
@@ -1,4 +1,4 @@
-sample,fastq_1,fastq_2,reference_assembly,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-SAMPLE1,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_2.fastq,https://raw.githubusercontent.com/phac-nml/snvphylnfc/dev/assets/reference.fasta,1.1,2.1,3.1,4.1,5.1,6.1,7.1,8.1
-SAMPLE2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_2.fastq,,1.1,2.2,3.2,4.2,5.2,6.2,7.1,8.2
-SAMPLE3,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_2.fastq,,1.2,2.2,3.3,4.3,5.3,6.2,,8.3
+sample,sample_name,fastq_1,fastq_2,reference_assembly,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
+SAMPLE1,A 1#,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_2.fastq,https://raw.githubusercontent.com/phac-nml/snvphylnfc/dev/assets/reference.fasta,1.1,2.1,3.1,4.1,5.1,6.1,7.1,8.1
+SAMPLE2,B2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_2.fastq,,1.1,2.2,3.2,4.2,5.2,6.2,7.1,8.2
+SAMPLE3,B2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_2.fastq,,1.2,2.2,3.3,4.3,5.3,6.2,,8.3
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -10,9 +10,14 @@
             "sample": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "meta": ["id"],
+                "meta": ["irida_id"],
                 "unique": true,
-                "errorMessage": "Sample name must be provided and cannot contain spaces"
+                "errorMessage": "Sample must be provided and cannot contain spaces"
+            },
+            "sample_name": {
+                "type": "string",
+                "meta": ["id", "id_alt"],
+                "errorMessage": "Sample name is optional, if provided will replace sample for filenames and outputs"
             },
             "fastq_1": {
                 "type": "string",

diff --git a/conf/iridanext.config b/conf/iridanext.config
@@ -1,6 +1,7 @@
 iridanext {
     enabled = true
     output {
+        idkey = "irida_id"
         path = "${params.outdir}/iridanext.output.json.gz"
         overwrite = true
         files {

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -15,5 +15,5 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = 'https://raw.githubusercontent.com/phac-nml/snvphylnfc/dev/assets/samplesheet.csv'
+    input = "${projectDir}/assets/samplesheet.csv"
 }
diff --git a/docs/usage.md b/docs/usage.md
@@ -14,19 +14,20 @@ You will need to create a samplesheet with information about the samples you wou
 
 ### Full samplesheet
 
-The input samplesheet can contain the following columns: `sample`, `fastq_1`, `fastq_2`, `reference_assembly`, and `metadata_1` - `metadata_8`. The sample IDs within a samplesheet should be unique.
+The input samplesheet can contain the following columns: `sample`, `sample_name`, `fastq_1`, `fastq_2`, `reference_assembly`, and `metadata_1` - `metadata_8`. The sample IDs within a samplesheet should be unique.
 
 A final samplesheet file consisting of both single- and paired-end data may look something like the one below.
 
 ```console
-sample,fastq_1,fastq_2,reference_assembly,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-SAMPLE1,/path/to/sample1_fastq1.fq,/path/to/sample1_fastq2.fq,/path/to/sample1_assembly.fa,,,,,,,,
-SAMPLE2,/path/to/sample2_fastq1.fq,,,,,,,,,,
+sample,sample_name,fastq_1,fastq_2,reference_assembly,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
+SAMPLE1,A1,/path/to/sample1_fastq1.fq,/path/to/sample1_fastq2.fq,/path/to/sample1_assembly.fa,,,,,,,,
+SAMPLE2,B2,/path/to/sample2_fastq1.fq,,,,,,,,,,
 ```
 
 | Column                       | Description                                                                                                                                                                            |
 | ---------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `sample`                     | Custom sample name. Samples should be unique within a samplesheet.                                                                                                                     |
+| `sample_name`                | Sample name used in outputs (filenames and sample names)                                                                                                                               |
 | `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`                    | (Optional) Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                  |
 | `reference_assembly`         | (Optional) Full path to a FASTA file representing a reference assembly derived from this sample. This field provides a method for selecting a reference genome for the whole pipeline. |

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -47,8 +47,7 @@
                 "reference_sample_id": {
                     "type": "string",
                     "fa_icon": "fas fa-file",
-                    "description": "The sample ID from which to use the associated FASTA-format assembly as a reference.",
-                    "pattern": "^\\S+$"
+                    "description": "The sample ID from which to use the associated FASTA-format assembly as a reference."
                 },
                 "refgenome": {
                     "type": "string",

diff --git a/tests/data/SAMPLE1.json.gz → tests/data/A_1_.json.gz b/tests/data/SAMPLE1.json.gz → tests/data/A_1_.json.gz
diff --git a/tests/data/SAMPLE1.simple.json.gz → tests/data/A_1_.simple.json.gz b/tests/data/SAMPLE1.simple.json.gz → tests/data/A_1_.simple.json.gz
diff --git a/tests/data/SAMPLE1_1.fastq → tests/data/A_1__1.fastq b/tests/data/SAMPLE1_1.fastq → tests/data/A_1__1.fastq
diff --git a/tests/data/SAMPLE1_2.fastq → tests/data/A_1__2.fastq b/tests/data/SAMPLE1_2.fastq → tests/data/A_1__2.fastq
diff --git a/tests/data/SAMPLE1_sorted.bam → tests/data/A_1__sorted.bam b/tests/data/SAMPLE1_sorted.bam → tests/data/A_1__sorted.bam
diff --git a/tests/data/SAMPLE2.simple.json.gz → tests/data/B2.simple.json.gz b/tests/data/SAMPLE2.simple.json.gz → tests/data/B2.simple.json.gz
diff --git a/tests/data/SAMPLE3.simple.json.gz → tests/data/B2_SAMPLE3.simple.json.gz b/tests/data/SAMPLE3.simple.json.gz → tests/data/B2_SAMPLE3.simple.json.gz
diff --git a/tests/data/SAMPLE3_sorted.bam → tests/data/B2_SAMPLE3_sorted.bam b/tests/data/SAMPLE3_sorted.bam → tests/data/B2_SAMPLE3_sorted.bam
diff --git a/tests/data/SAMPLE2_sorted.bam → tests/data/B2_sorted.bam b/tests/data/SAMPLE2_sorted.bam → tests/data/B2_sorted.bam
diff --git a/tests/data/samplesheets/samplesheet1.csv b/tests/data/samplesheets/samplesheet1.csv
@@ -1,4 +1,4 @@
-sample,fastq_1,fastq_2,reference_assembly,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-SAMPLE1,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_2.fastq,https://raw.githubusercontent.com/phac-nml/snvphylnfc/dev/assets/reference.fasta,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
-SAMPLE2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_2.fastq,,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
-SAMPLE3,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_2.fastq,,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8
+sample,sample_name,fastq_1,fastq_2,reference_assembly,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
+SAMPLE1,A 1#,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_2.fastq,https://raw.githubusercontent.com/phac-nml/snvphylnfc/dev/assets/reference.fasta,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
+SAMPLE2,B2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_2.fastq,,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
+SAMPLE3,B2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_2.fastq,,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8
diff --git a/tests/data/samplesheets/samplesheet_few-metadata.csv b/tests/data/samplesheets/samplesheet_few-metadata.csv
@@ -1,5 +1,5 @@
-sample,fastq_1,fastq_2,reference_assembly,metadata_1,metadata_2,metadata_3
-SAMPLE1,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_2.fastq,https://raw.githubusercontent.com/phac-nml/snvphylnfc/dev/assets/reference.fasta,1.1,2.1,3.1
-SAMPLE2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_2.fastq,,,2.2,3.2
-SAMPLE3,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_2.fastq,,1.3,2.3,,
+sample,sample_name,fastq_1,fastq_2,reference_assembly,metadata_1,metadata_2,metadata_3
+SAMPLE1,A 1#,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_2.fastq,https://raw.githubusercontent.com/phac-nml/snvphylnfc/dev/assets/reference.fasta,1.1,2.1,3.1
+SAMPLE2,B2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_2.fastq,,,2.2,3.2
+SAMPLE3,B2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_2.fastq,,1.3,2.3,,
 
diff --git a/tests/data/samplesheets/samplesheet_little-metadata.csv b/tests/data/samplesheets/samplesheet_little-metadata.csv
@@ -1,4 +1,4 @@
-sample,fastq_1,fastq_2,reference_assembly,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-SAMPLE1,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_2.fastq,https://raw.githubusercontent.com/phac-nml/snvphylnfc/dev/assets/reference.fasta,,,,1.4,,,,
-SAMPLE2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_2.fastq,,,,,,,,,
-SAMPLE3,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_2.fastq,,3.1,3.2,,,,,,3.8
+sample,sample_name,fastq_1,fastq_2,reference_assembly,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
+SAMPLE1,A 1#,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_2.fastq,https://raw.githubusercontent.com/phac-nml/snvphylnfc/dev/assets/reference.fasta,,,,1.4,,,,
+SAMPLE2,B2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_2.fastq,,,,,,,,,
+SAMPLE3,B2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_2.fastq,,3.1,3.2,,,,,,3.8
diff --git a/tests/data/samplesheets/samplesheet_no-metadata.csv b/tests/data/samplesheets/samplesheet_no-metadata.csv
@@ -1,4 +1,4 @@
-sample,fastq_1,fastq_2,reference_assembly
-SAMPLE1,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_2.fastq,https://raw.githubusercontent.com/phac-nml/snvphylnfc/dev/assets/reference.fasta
-SAMPLE2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_2.fastq,,
-SAMPLE3,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_2.fastq,,
+sample,sample_name,fastq_1,fastq_2,reference_assembly
+SAMPLE1,A 1#,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/a_2.fastq,https://raw.githubusercontent.com/phac-nml/snvphylnfc/dev/assets/reference.fasta
+SAMPLE2,B2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/b_2.fastq,,
+SAMPLE3,B2,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_1.fastq,https://raw.githubusercontent.com/phac-nml/snvphyl-galaxy-cli/development/example-data/fastqs/c_2.fastq,,