Update test inputs

workflow/main.nf

-/*
- * Copyright (c) 2023. The University of Texas Southwestern Medical Center
- *
- *   This file is part of the BioHPC Workflow Platform
- *
- * This is a workflow package to run cellranger count on fastq files from single cell RNA data.
- *
- * @authors
- * John Lafin
- *
- */
-
-
-// Parameters for input values
-params.sample_sheet = "${projectDir}/../test_data/sample_sheet.csv"
-params.fastq = "${projectDir}/../test_data"
-params.outDir = "${projectDir}/output"
-params.astrocyte = false
-
-// Run cellranger count
-process cr_count {
-    publishDir "${outDir}", mode: 'copy'
-    module 'cellranger/7.1.0'
-    module 'singularity/3.9.9'
-    errorStrategy 'ignore'
-
-    input: 
-        tuple val(sample), val(ref), val(expectCells), val(chemistry), val(introns), val(noBam)
-        path(fastq)
-        path(outDir)
-        
-    output:
-        tuple val(sample), path("${sample}/outs/**")
-
-    script:
-        // Check reference
-        if (params.astrocyte)  {
-            switch (ref) {
-                case "hg38":
-                    ref = file("/project/apps_database/cellranger/refdata-gex-GRCh38-2020-A")
-                    break
-                case "mm10":
-                    ref = file("/project/apps_database/cellranger/refdata-gex-mm10-2020-A")
-                    break
-                default:
-                    ref = file(ref)
-            }
-        }
-        
-        if ( ref.isEmpty() ) {
-            error "Error: Missing reference. Please provide one of the options outlined in the documentation."
-        }
-
-        // Run Cell Ranger count
-        if( expectCells == 0 )
-            if( noBam )
-            """
-            cellranger count --id=$sample \
-                            --transcriptome=$ref \
-                            --fastqs=. \
-                            --sample=$sample \
-                            --chemistry=$chemistry \
-                            --include-introns=$introns \
-                            --no-bam
-            """
-            else
-            """
-            cellranger count --id=$sample \
-                            --transcriptome=$ref \
-                            --fastqs=. \
-                            --sample=$sample \
-                            --chemistry=$chemistry \
-                            --include-introns=$introns
-            """
-
-        else if( expectCells > 0)
-            if( noBam )
-            """
-            cellranger count --id=$sample \
-                            --transcriptome=$ref \
-                            --fastqs=. \
-                            --sample=$sample \
-                            --expect-cells=$expectCells \
-                            --chemistry=$chemistry \
-                            --include-introns=$introns \
-                            --no-bam
-            """
-            else
-            """
-            cellranger count --id=$sample \
-                            --transcriptome=$ref \
-                            --fastqs=. \
-                            --sample=$sample \
-                            --expect-cells=$expectCells \
-                            --chemistry=$chemistry \
-                            --include-introns=$introns
-            """
-}
-
-workflow {
-    // Parse sample sheet and run cellranger count
-    fastq = channel.fromPath(params.fastq).collect()
-    outDir = channel.value(params.outDir)
-    input = channel.fromPath(params.sample_sheet) \
-        | splitCsv(header: true) \
-        | map{ row -> tuple( row.sample, row.reference, row.expectCells, row.chemistry, row.introns, row.noBam ) }
-    cr_count(input, fastq, outDir)
-}
+/*
+ * Copyright (c) 2023. The University of Texas Southwestern Medical Center
+ *
+ *   This file is part of the BioHPC Workflow Platform
+ *
+ * This is a workflow package to run cellranger count on fastq files from single cell RNA data.
+ *
+ * @authors
+ * John Lafin
+ *
+ */
+
+
+// Parameters for input values
+params.sample_sheet = "${projectDir}/../test_data/sample_sheet.csv"
+params.fastq = "${projectDir}/../test_data/fastqs"
+params.outDir = "${projectDir}/output"
+params.astrocyte = true
+
+// Run cellranger count
+process cr_count {
+    publishDir "${outDir}", mode: 'copy'
+    module 'cellranger/7.1.0'
+    module 'singularity/3.9.9'
+    errorStrategy 'ignore'
+
+    input: 
+        tuple val(sample), val(ref), val(expectCells), val(chemistry), val(introns), val(noBam)
+        path(fastq)
+        path(outDir)
+        
+    output:
+        tuple val(sample), path("${sample}/outs/**")
+
+    script:
+        // Check reference
+        if (params.astrocyte)  {
+            switch (ref) {
+                case "hg38":
+                    ref = file("/project/apps_database/cellranger/refdata-gex-GRCh38-2020-A")
+                    break
+                case "mm10":
+                    ref = file("/project/apps_database/cellranger/refdata-gex-mm10-2020-A")
+                    break
+                default:
+                    ref = file(ref)
+            }
+        }
+        
+        if ( ref.isEmpty() ) {
+            error "Error: Missing reference. Please provide one of the options outlined in the documentation."
+        }
+
+        // Run Cell Ranger count
+        if( expectCells == 0 )
+            if( noBam )
+            """
+            cellranger count --id=$sample \
+                            --transcriptome=$ref \
+                            --fastqs=. \
+                            --sample=$sample \
+                            --chemistry=$chemistry \
+                            --include-introns=$introns \
+                            --no-bam
+            """
+            else
+            """
+            cellranger count --id=$sample \
+                            --transcriptome=$ref \
+                            --fastqs=. \
+                            --sample=$sample \
+                            --chemistry=$chemistry \
+                            --include-introns=$introns
+            """
+
+        else if( expectCells > 0)
+            if( noBam )
+            """
+            cellranger count --id=$sample \
+                            --transcriptome=$ref \
+                            --fastqs=. \
+                            --sample=$sample \
+                            --expect-cells=$expectCells \
+                            --chemistry=$chemistry \
+                            --include-introns=$introns \
+                            --no-bam
+            """
+            else
+            """
+            cellranger count --id=$sample \
+                            --transcriptome=$ref \
+                            --fastqs=. \
+                            --sample=$sample \
+                            --expect-cells=$expectCells \
+                            --chemistry=$chemistry \
+                            --include-introns=$introns
+            """
+}
+
+workflow {
+    // Parse sample sheet and run cellranger count
+    fastq = channel.fromPath(params.fastq).collect()
+    outDir = channel.value(params.outDir)
+    input = channel.fromPath(params.sample_sheet) \
+        | splitCsv(header: true) \
+        | map{ row -> tuple( row.sample, row.reference, row.expectCells, row.chemistry, row.introns, row.noBam ) }
+    cr_count(input, fastq, outDir)
+}
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