From 24156659d894a6ce4c8f4383f48560f45e5f62d7 Mon Sep 17 00:00:00 2001
From: nschcolnicov <nico.schcolnicov@gmail.com>
Date: Wed, 16 Oct 2024 19:43:57 +0000
Subject: [PATCH] Installed samshee from nf-core

---
 modules.json                                  |  5 +++++
 modules/nf-core/samshee/environment.yml       |  6 ++---
 modules/nf-core/samshee/main.nf               |  1 +
 modules/nf-core/samshee/tests/main.nf.test    | 22 ++++++++++++++++---
 .../nf-core/samshee/tests/main.nf.test.snap   |  6 ++---
 modules/nf-core/samshee/tests/nextflow.config |  6 ++++-
 6 files changed, 35 insertions(+), 11 deletions(-)

diff --git a/modules.json b/modules.json
index 91bf80bf..ae24885e 100644
--- a/modules.json
+++ b/modules.json
@@ -65,6 +65,11 @@
                         "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
                         "installed_by": ["modules"]
                     },
+                    "samshee": {
+                        "branch": "master",
+                        "git_sha": "3c464e75051db485c1b37ab9f1ea2182fb3d3533",
+                        "installed_by": ["modules"]
+                    },
                     "seqtk/sample": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
diff --git a/modules/nf-core/samshee/environment.yml b/modules/nf-core/samshee/environment.yml
index b46b46a6..35a8e2e7 100644
--- a/modules/nf-core/samshee/environment.yml
+++ b/modules/nf-core/samshee/environment.yml
@@ -2,7 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - python>=3.9
-  - pip
-  - pip: # FIXME https://github.com/nf-core/modules/issues/5814
-      - samshee==0.2.1
+  - bioconda::samshee=0.2.1
+  - python=3.13.0
diff --git a/modules/nf-core/samshee/main.nf b/modules/nf-core/samshee/main.nf
index 70bbd690..6d7ba2e6 100644
--- a/modules/nf-core/samshee/main.nf
+++ b/modules/nf-core/samshee/main.nf
@@ -25,6 +25,7 @@ process SAMSHEE {
     # Run validation command and capture output
     python -m samshee $samplesheet \
     $args \
+    $arg_file_schema_validator \
     > ${samplesheet.baseName}_formatted.csv
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/samshee/tests/main.nf.test b/modules/nf-core/samshee/tests/main.nf.test
index 62c8994e..5bec682f 100644
--- a/modules/nf-core/samshee/tests/main.nf.test
+++ b/modules/nf-core/samshee/tests/main.nf.test
@@ -12,12 +12,18 @@ nextflow_process {
 
         when {
             params {
-                v1_schema = true
+                v1_schema             = true
+                json_schema_validator = '{"required": ["Data"]}'
+                name_schema_validator = null
             }
             process {
                 """
                 input[0] = [ [ id: 'test', lane:1 ], file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/miseq_35147139/miseq_35147139_samplesheet.csv", checkIfExists: true) ]
-                input[1] = []
+                input[1] = file("schema.json")
+                new File("schema.json").text = '''{
+                    "\$schema": "https://json-schema.org/draft/2020-12/schema",
+                    "required": ["Settings"]
+                }'''
                 """
             }
         }
@@ -31,6 +37,11 @@ nextflow_process {
     test("test samplesheet_v2") {
 
         when {
+            params {
+                v1_schema             = null
+                json_schema_validator = null
+                name_schema_validator = '{"$ref": "urn:samshee:illuminav2/v1"}'
+            }
             process {
                 """
                 input[0] = [ [ id: 'test', lane:1 ], file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NextSeq2000/SampleSheet.csv", checkIfExists: true) ]
@@ -51,9 +62,14 @@ nextflow_process {
         options "-stub"
 
         when {
+            params {
+                v1_schema             = null
+                json_schema_validator = null
+                name_schema_validator = null
+            }
             process {
                 """
-                input[0] = [ [ id: 'test', lane:1 ], file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NextSeq2000/SampleSheet.csv", checkIfExists: true), [] ]
+                input[0] = [ [ id: 'test', lane:1 ], file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NextSeq2000/SampleSheet.csv", checkIfExists: true) ]
                 input[1] = []
                 """
             }
diff --git a/modules/nf-core/samshee/tests/main.nf.test.snap b/modules/nf-core/samshee/tests/main.nf.test.snap
index e00d8af0..b3729eba 100644
--- a/modules/nf-core/samshee/tests/main.nf.test.snap
+++ b/modules/nf-core/samshee/tests/main.nf.test.snap
@@ -32,7 +32,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T12:33:58.766224702"
+        "timestamp": "2024-10-16T15:25:40.722007136"
     },
     "test samplesheet_v1": {
         "content": [
@@ -67,7 +67,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T12:30:57.470221349"
+        "timestamp": "2024-10-16T15:25:02.353128191"
     },
     "test samplesheet_v2": {
         "content": [
@@ -102,6 +102,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T12:31:16.99133356"
+        "timestamp": "2024-10-16T15:25:24.540910786"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/samshee/tests/nextflow.config b/modules/nf-core/samshee/tests/nextflow.config
index aa0e36ad..ecf1ff66 100644
--- a/modules/nf-core/samshee/tests/nextflow.config
+++ b/modules/nf-core/samshee/tests/nextflow.config
@@ -1,5 +1,9 @@
 process {
     withName: SAMSHEE {
-        ext.args = { params.v1_schema ? "--output-format sectioned" : "" }
+        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()
     }
 }