PR comments on module

nf-core · Oct 15, 2024 · 9b33143 · 9b33143
1 parent 6e615b9
commit 9b33143
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Showing 5 changed files with 14 additions and 23 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -234,6 +234,9 @@ process {
     }
 
     withName: SAMSHEE {
+        ext.json_schema_validator = { params.json_schema_validator ? "--schema '${params.json_schema_validator}'" : "" }
+        ext.name_schema_validator = { params.name_schema_validator ? "--schema '${params.name_schema_validator}'" : "" }
+        ext.v1                    = { params.v1_schema ? "--output-format sectioned" : "" }
         errorStrategy = "terminate"
         publishDir = [
             path: { "${params.outdir}/" },

diff --git a/conf/test_full.config b/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
 }
diff --git a/modules/nf-core/samshee/main.nf b/modules/nf-core/samshee/main.nf
diff --git a/modules/nf-core/samshee/meta.yml b/modules/nf-core/samshee/meta.yml
diff --git a/workflows/demultiplex.nf b/workflows/demultiplex.nf
@@ -63,8 +63,6 @@ workflow DEMULTIPLEX {
     ch_multiqc_files         = Channel.empty()
     ch_multiqc_reports       = Channel.empty()
     checkqc_config           = params.checkqc_config        ? Channel.fromPath(params.checkqc_config, checkIfExists: true)        : [] // file checkqc_config.yaml
-    ch_json_schema_validator = params.json_schema_validator ? Channel.value(params.json_schema_validator)                         : [] // string schema in json format
-    ch_name_schema_validator = params.name_schema_validator ? Channel.value(params.name_schema_validator)                         : [] // string schema name
     ch_file_schema_validator = params.file_schema_validator ? Channel.fromPath(params.file_schema_validator, checkIfExists: true) : [] // file schema.json
 
     // Remove adapter from Illumina samplesheet to avoid adapter trimming in demultiplexer tools
@@ -94,8 +92,6 @@ workflow DEMULTIPLEX {
     if (!("samshee" in skip_tools) && (params.demultiplexer in ["bcl2fastq", "bclconvert", "mkfastq"])){
         SAMSHEE (
             ch_samplesheet.map{ meta, samplesheet, flowcell, lane -> [meta,samplesheet] },
-            ch_json_schema_validator,
-            ch_name_schema_validator,
             ch_file_schema_validator
         )
         ch_versions = ch_versions.mix(SAMSHEE.out.versions)