Some improvements but not working :(

nf-core · Mar 8, 2024 · 8c68e1d · 8c68e1d
1 parent c71189f
commit 8c68e1d
Showing 1 changed file with 23 additions and 33 deletions.
diff --git a/subworkflows/local/quantify_pseudo_alignment/tests/main.nf.test b/subworkflows/local/quantify_pseudo_alignment/tests/main.nf.test
@@ -3,23 +3,22 @@ nextflow_workflow {
     name "Test Workflow QUANTIFY_PSEUDO_ALIGNMENT"
     script "../main.nf"
     workflow "QUANTIFY_PSEUDO_ALIGNMENT"
-    config './nextflow.config'
 
     tag 'SALMON_QUANT'
     tag 'KALLISTO_QUANT'
     tag 'CUSTOM_TX2GENE'
     tag 'TXIMETA_TXIMPORT'
     tag 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT'
 
-    test("salmon") {
+    // test("salmon") {
 
         setup {
             run("SALMON_INDEX") {
                 script "../../../../modules/nf-core/salmon/index/main.nf"
                 process {
                     """
                     input[0] = Channel.of([file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)])
-                    input[1] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true)])
                     """
                 }
             }
@@ -28,33 +27,28 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                def fileContents = [
-                    'sample,fastq_1,fastq_2,strandedness',
-                    'test,s3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/genomics/sarscov2/illumina/fastq/test_1.fastq.gz,s3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/genomics/sarscov2/illumina/fastq/test_2.fastq.gz,auto'
+                input[0]  = [
+                    [ id: 'samplesheet' ],
+                    file(params.pipelines_testdata_base_path + '/csv/samplesheet_micro.csv', checkIfExists: true)
                 ]
-                def samplesheetFile = file("${workDir}/samplesheetFile.txt")
-                samplesheetFile.withWriter{ out ->
-                    fileContents.each {out.println it}
-                }
-                input[0]  = samplesheetFile
                 input[1]  = [
                     [ id: 'meta' ],
                     [
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                        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[2]  = SALMON_INDEX.out.index
-                input[3]  = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true))
-                input[4]  = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true))
+                input[3]  = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true))
+                input[4]  = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true))
                 input[5]  = 'gene_id'
                 input[6]  = 'gene_name'
                 input[7]  = 'salmon'
                 input[8]  = true
                 input[9]  = ''
                 input[10] = null
                 input[11] = null
-                """.stripIndent()
+                """
             }
         }
 
@@ -76,43 +70,39 @@ nextflow_workflow {
                     """
                     input[0] = Channel.of([
                         [ id:'transcriptome' ], // meta map
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true)
                     ])
                     """
                 }
             }
         }
 
+
         when {
             workflow {
                 """
-                def fileContents = [
-                    'sample,fastq_1,fastq_2,strandedness',
-                    'test,SRR6357070_1.fastq.gz,SRR6357070_2.fastq.gz,auto'
+                input[0]  = [
+                    [ id: 'samplesheet' ],
+                    file(params.pipelines_testdata_base_path + '/csv/samplesheet_micro.csv', checkIfExists: true)
                 ]
-                def samplesheetFile = file("${workDir}/samplesheetFile.txt")
-                samplesheetFile.withWriter{ out ->
-                    fileContents.each {out.println it}
-                }
-                input[0]  = samplesheetFile
                 input[1]  = [
-                    [ id: 'meta' ],
+                    [ id: 'test' ],
                     [
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                        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[2]  = KALLISTO_INDEX.out.index
-                input[3]  = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true))
-                input[4]  = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true))
+                input[3]  = Channel.of(file(params.modules_testdata_base_path +  "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true))
+                input[4]  = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.gtf", checkIfExists: true))
                 input[5]  = 'gene_id'
                 input[6]  = 'gene_name'
                 input[7]  = 'kallisto'
                 input[8]  = null
                 input[9]  = null
-                input[10] = null
-                input[11] = null
-                """.stripIndent()
+                input[10] = []
+                input[11] = []
+                """
             }
         }