From 71df2e6b45cd8812a4d7c88afbc16c06a61e988d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 27 Jan 2025 19:30:12 +0100
Subject: [PATCH] rescue SAMPLESHEET_TO_CHANNEL test

---
 .../samplesheet_to_channel/tests/main.nf.test | 58 +++++++------------
 1 file changed, 22 insertions(+), 36 deletions(-)

diff --git a/subworkflows/local/samplesheet_to_channel/tests/main.nf.test b/subworkflows/local/samplesheet_to_channel/tests/main.nf.test
index e1c8682d27..e306558c77 100644
--- a/subworkflows/local/samplesheet_to_channel/tests/main.nf.test
+++ b/subworkflows/local/samplesheet_to_channel/tests/main.nf.test
@@ -10,44 +10,32 @@ nextflow_workflow {
             }
             workflow {
                 """
-                // define inputs of the workflow here. Example:
-                input[0] = Channel.of([
-                    ['patient':'test', 'sample':'test',
-                    'sex':'XX', 'status':0, 'lane':'test_L1'],
+                input[0] = Channel.of([ // samplesheet
+                    ['patient':'test', 'sample':'test', 'sex':'XX', 'status':0, 'lane':'test_L1'],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
                     [], [], [], [], [], [], [], [], []
                 ])
-                input[1] = 'bwa-mem' // aligner
-                input[2] = [] // ascat_alleles
-                input[3] = [] // ascat_loci
-                input[4] = [] // ascat_loci_gc
-                input[5] = [] // ascat_loci_rt
-                input[6] = [] // bcftools_annotations
-                input[7] = [] // bcftools_annotations_tbi
-                input[8] = [] // bcftools_header_lines
-                input[9] = false // build_only_index
-                input[10] = [] // dbsnp
-                input[11] = [] // fasta
-                input[12] = [] // germline_resource
-                input[13] = [] // intervals
-                input[14] = false // joint_germline
-                input[15] = false // joint_mutect2
-                input[16] = [] // known_indels
-                input[17] = [] // known_snps
-                input[18] = false // no_intervals
-                input[19] = [] // pon
-                input[20] = 'variant' // sentieon_dnascope_emit_mode
-                input[21] = 'variant' // sentieon_haplotyper_emit_mode
-                input[22] = '' // seq_center
-                input[23] = 'ILLUMINA' // seq_platform
-                input[24] = 'baserecalibrator' // skip_tools
-                input[25] = [] // snpeff_cache
-                input[26] = 'WBcel235.105' // snpeff_db
-                input[27] = 'mapping' // step
-                input[28] = 'strelka' // tools
-                input[29] = [] // umi_read_structure
-                input[30] = false // wes
+                input[1] = Channel.of([ // references
+                    ['id':'genome', 'vcf':[]],
+                    []
+                ])
+                input[2] = 'bwa-mem' // aligner
+                input[3] = [] // bcftools_annotations
+                input[4] = [] // bcftools_annotations_tbi
+                input[5] = [] // bcftools_header_lines
+                input[6] = false // joint_germline
+                input[7] = false // joint_mutect2
+                input[8] = false // no_intervals
+                input[9] = 'variant' // sentieon_dnascope_emit_mode
+                input[10] = 'variant' // sentieon_haplotyper_emit_mode
+                input[11] = '' // seq_center
+                input[12] = 'ILLUMINA' // seq_platform
+                input[13] = 'baserecalibrator' // skip_tools
+                input[14] = 'mapping' // step
+                input[15] = 'strelka' // tools
+                input[16] = [] // umi_read_structure
+                input[17] = false // wes
                 """
             }
         }
@@ -56,7 +44,5 @@ nextflow_workflow {
             assert workflow.success
             assert snapshot(workflow.out).match()
         }
-
     }
-
 }