Update samshee

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#275](https://github.com/nf-core/demultiplex/pull/275) Update samshee module from nf-core.
 - [#276](https://github.com/nf-core/demultiplex/pull/276) Template update for nf-core/tools v3.0.2
 
 ### `Fixed`

conf/modules.config

@@ -231,9 +231,18 @@ process {
             mode: params.publish_dir_mode
         ]
     }
-    // Samshee should fail the entire pipeline immediately as it validated the illumina samplesheet to be valid before the pipeline runs. As such, it should not be running more than once & if it fails should stop the pipeline
     withName: SAMSHEE {
+        ext.args = [
+            params.json_schema_validator ? "--schema '${params.json_schema_validator}'" : "",
+            params.name_schema_validator ? "--schema '${params.name_schema_validator}'" : "",
+            params.v1_schema ? "--output-format sectioned" : "",
+        ].join(" ").trim()
         errorStrategy = "terminate"
+        publishDir = [
+            path: { "${params.outdir}/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 }
 

conf/test_full.config

@@ -17,5 +17,5 @@ params {
     // Input data
     input         = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/samplesheet_full.csv'
     demultiplexer = 'bcl2fastq'
-    skip_tools    = 'samshee'
+    v1_schema     = true
 }

docs/usage.md

@@ -97,9 +97,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
-:::warning
-Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
-:::
+> [!WARNING]
+> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
 
 The above pipeline run specified with a params file in yaml format:
 
@@ -130,7 +129,16 @@ The trimming process in our demultiplexing pipeline has been updated to ensure c
 
 ## samshee (Samplesheet validator)
 
-samshee ensures the integrity of Illumina v2 Sample Sheets by allowing users to apply custom validation rules. The module can be used together with the parameter `--validator_schema`, which accepts a JSON schema validator file. Users can specify this file to enforce additional validation rules beyond the default ones provided by the tool. To use this feature, simply provide the path to the JSON schema validator file via the `--validator_schema` parameter in the pipeline configuration. This enables tailored validation of Sample Sheets to meet specific requirements or standards relevant to your sequencing workflow. For more information about the tool or how to write the schema JSON file, please refer to [Samshee on GitHub](https://github.com/lit-regensburg/samshee).
+samshee ensures the integrity of Illumina v2 Sample Sheets by allowing users to apply custom validation rules. The module can be used together with the parameter `--json_schema_validator`, which accepts a JSON schema validation string; the `--name_schema_validator`, which accepts a schema name string; and the `--file_schema_validator` which accepts a JSON schema validation file. Users can specify additional validation rules beyond the default ones provided by the tool using all or any of these parameters, this enables tailored validation of Sample Sheets to meet specific requirements or standards relevant to your sequencing workflow. For more information refer to [Samshee on GitHub](https://github.com/lit-regensburg/samshee).
+
+> [!NOTE]
+> Samshee assumes all illumina samplesheets are v2. If working with samples that have an illumina samplesheet v1 set the parameter `--v1_schema` to true.
+> When indicating `--json_schema_validator` or `--name_schema_validator`, please note that it expects a JSON reference value in string format. For example:
+>
+> ```bash
+> --json_schema_validator '{"required": ["Data"]}'
+> --name_schema_validator '{"$ref": "urn:samshee:illuminav2/v1"}'
+> ```
 
 ### Updating the pipeline
 
@@ -150,25 +158,22 @@ This version number will be logged in reports when you run the pipeline, so that
 
 To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
-:::tip
-If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
-:::
+> [!TIP]
+> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
 
 ## Core Nextflow arguments
 
-:::note
-These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
-:::
+> [!NOTE]
+> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
 
 ### `-profile`
 
 Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
 
 Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
 
-:::info
-We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
-:::
+> [!NOTE]
+> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 
 The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
 

modules.json

@@ -65,6 +65,11 @@
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
+                    "samshee": {
+                        "branch": "master",
+                        "git_sha": "3c464e75051db485c1b37ab9f1ea2182fb3d3533",
+                        "installed_by": ["modules"]
+                    },
                     "seqtk/sample": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",