Addressing PR comments

nf-core · Oct 15, 2024 · 8c80296 · 8c80296
1 parent 31b03e1
commit 8c80296
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Showing 5 changed files with 21 additions and 36 deletions.
diff --git a/modules/nf-core/samshee/main.nf b/modules/nf-core/samshee/main.nf
@@ -4,14 +4,12 @@ process SAMSHEE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://community.wave.seqera.io/library/pip_samshee:733e11f3377fc2e3' :
-        'community.wave.seqera.io/library/pip_samshee:733e11f3377fc2e3' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/65/659cdc3068a6fbce17ccb199bb3afc8600c65940743c1a0214b3bf0eed4df1a3/data' :
+        'community.wave.seqera.io/library/pip_samshee:9b655e3c18eee356' }"
 
     input:
     tuple val(meta), path(samplesheet)
-    val(json_schema_validator)  // optional
-    val(name_schema_validator)  // optional
-    path(file_schema_validator) // optional
+    path(file_schema_validator)
 
     output:
     tuple val(meta), path("*_formatted.csv"), emit: samplesheet
@@ -21,18 +19,11 @@ process SAMSHEE {
     task.ext.when == null || task.ext.when
 
     script:
-    def arg_json_schema_validator = json_schema_validator ? "--schema '${json_schema_validator}'"                         : ""
-    def arg_name_schema_validator = name_schema_validator ? "--schema '${name_schema_validator}'"                         : ""
-    def arg_file_schema_validator = file_schema_validator ? "--schema '{\"\$ref\": \"file:${file_schema_validator}\"}'" : ""
-    def arg_v1_schema             = params.v1_schema      ? "--output-format sectioned"                                   : ""
+    def arg_file_schema_validator = file_schema_validator ? "--schema '{\"\$ref\": \"file:${file_schema_validator}\"}'"   : ""
     def args = task.ext.args ?: ""
     """
     # Run validation command and capture output
     python -m samshee $samplesheet \
-    $arg_json_schema_validator \
-    $arg_name_schema_validator \
-    $arg_file_schema_validator \
-    $arg_v1_schema \
     $args \
     > ${samplesheet.baseName}_formatted.csv
 

diff --git a/modules/nf-core/samshee/meta.yml b/modules/nf-core/samshee/meta.yml
@@ -23,15 +23,9 @@ input:
         type: file
         description: "illumina v2 samplesheet"
         pattern: "*.{csv}"
-  - - json_schema_validator:
-        type: string
-        description: "String in JSON format used additional samplesheet validation settings"
-  - - name_schema_validator:
-        type: string
-        description: "Schema name used additional samplesheet validation settings"
   - - file_schema_validator:
         type: string
-        description: "JSON file used additional samplesheet validation settings"
+        description: "Optional JSON file used additional samplesheet validation settings"
 output:
   - samplesheet:
       - meta:

diff --git a/modules/nf-core/samshee/tests/main.nf.test b/modules/nf-core/samshee/tests/main.nf.test
@@ -3,6 +3,7 @@ nextflow_process {
     name "Test Process samshee"
     script "../main.nf"
     process "SAMSHEE"
+    config "./nextflow.config"
     tag "modules"
     tag "modules_nfcore"
     tag "samshee"
@@ -16,9 +17,7 @@ nextflow_process {
             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] = '{"required": ["Data"]}'
-                input[2] = []
-                input[3] = []
+                input[1] = []
                 """
             }
         }
@@ -36,8 +35,6 @@ nextflow_process {
                 """
                 input[0] = [ [ id: 'test', lane:1 ], file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NextSeq2000/SampleSheet.csv", checkIfExists: true) ]
                 input[1] = []
-                input[2] = '{"\$ref": "urn:samshee:illuminav2/v1"}'
-                input[3] = []
                 """
             }
         }
@@ -58,8 +55,6 @@ nextflow_process {
                 """
                 input[0] = [ [ id: 'test', lane:1 ], file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NextSeq2000/SampleSheet.csv", checkIfExists: true), [] ]
                 input[1] = []
-                input[2] = []
-                input[3] = []
                 """
             }
         }

diff --git a/modules/nf-core/samshee/tests/main.nf.test.snap b/modules/nf-core/samshee/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8fbb7f500f23ab9ecff6ad5b9f15f14a"
+                    "versions.yml:md5,77af0194d386117bf52aaabdf350a976"
                 ],
                 "samplesheet": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8fbb7f500f23ab9ecff6ad5b9f15f14a"
+                    "versions.yml:md5,77af0194d386117bf52aaabdf350a976"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-10T19:18:20.176809754"
+        "timestamp": "2024-10-15T12:33:58.766224702"
     },
     "test samplesheet_v1": {
         "content": [
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8fbb7f500f23ab9ecff6ad5b9f15f14a"
+                    "versions.yml:md5,77af0194d386117bf52aaabdf350a976"
                 ],
                 "samplesheet": [
                     [
@@ -59,15 +59,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8fbb7f500f23ab9ecff6ad5b9f15f14a"
+                    "versions.yml:md5,77af0194d386117bf52aaabdf350a976"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-10T19:17:58.422458873"
+        "timestamp": "2024-10-15T12:30:57.470221349"
     },
     "test samplesheet_v2": {
         "content": [
@@ -82,7 +82,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8fbb7f500f23ab9ecff6ad5b9f15f14a"
+                    "versions.yml:md5,77af0194d386117bf52aaabdf350a976"
                 ],
                 "samplesheet": [
                     [
@@ -94,14 +94,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8fbb7f500f23ab9ecff6ad5b9f15f14a"
+                    "versions.yml:md5,77af0194d386117bf52aaabdf350a976"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-10T19:18:08.736465443"
+        "timestamp": "2024-10-15T12:31:16.99133356"
     }
 }
diff --git a/modules/nf-core/samshee/tests/nextflow.config b/modules/nf-core/samshee/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: SAMSHEE {
+        ext.args = { params.v1_schema ? "--output-format sectioned" : "" }
+    }
+}