Merge branch 'main' of https://github.com/nf-core/seqinspector into a…

…dd-modules
nf-core · Mar 22, 2024 · b883059 · b883059
2 parents e39be60 + d169eef
commit b883059
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -41,7 +41,7 @@
             },
             "rundir": {
                 "type": "string",
-                "format": "directory-path",
+                "format": "path",
                 "exists": true,
                 "errorMessage": "Run directory must be a path",
                 "meta": ["rundir"]

diff --git a/conf/test.config b/conf/test.config
@@ -22,7 +22,7 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
+    input  = 'https://raw.githubusercontent.com/KarNair/test-datasets/seqinspector/testdata/MiSeq/samplesheet.csv'
 
     // Genome references
     genome = 'R64-1-1'

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -84,7 +84,7 @@ workflow PIPELINE_INITIALISATION {
         .fromSamplesheet("input") // Validates samplesheet against $projectDir/assets/schema_input.json. Path to validation schema is defined by $projectDir/nextflow_schema.json
         .map {
             meta, fastq_1, fastq_2 ->
-                def id_string = "${meta.sample}_${meta.group ?: "ungrouped"}_${meta.lane}"
+                def id_string = "${meta.sample}_${meta.project ?: "ungrouped"}_${meta.lane}"
                 def updated_meta = meta + [ id: id_string ]
                 if (!fastq_2) {
                     return [ updated_meta.id, updated_meta + [ single_end:true ], [ fastq_1 ] ]