Update tests

software/trimgalore/test/main.nf

@@ -1,27 +1,66 @@
 #!/usr/bin/env nextflow
-nextflow.preview.dsl=2
 
-params.outdir = "."             // gets set in the nextflow.config files (to './results/trim_galore')
-params.verbose = false
-params.trim_galore_args = ''
-// trim_galore_args are best passed into the workflow in the following manner, e.g.:
-// --trim_galore_args="--clip_r1 10 --clip_r2 15 -j 2"
+nextflow.enable.dsl = 2
 
-if (params.verbose){
-    println ("[WORKFLOW] TRIM GALORE ARGS: "      + params.trim_galore_args)
+include { TRIMGALORE } from '../main.nf'
+
+/*
+ * Test with single-end data
+ */
+workflow test_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
+
+    TRIMGALORE ( input, [ publish_dir:'test_single_end' ] )
 }
 
-// TODO: check the output files in some way
-// include '../../../tests/functions/check_process_outputs.nf'
-include '../main.nf'  // params (clip_r1: 6, clip_r2: 10) // how to pass additional parameters
+/*
+ * Test with paired-end data
+ */
+workflow test_paired_end {
 
-ch_read_files = Channel
-  .fromFilePairs('../../../test-datasets/test*{1,2}.fastq.gz',size:-1)
-  // .view()  // to check whether the input channel works
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
+                file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
+
+    TRIMGALORE ( input, [ publish_dir:'test_paired_end' ] )
+}
 
 workflow {
-
-    main:
-        TRIM_GALORE (ch_read_files, params.outdir, params.trim_galore_args, params.verbose)
-
+    test_single_end()
+    test_paired_end()
 }
+
+
+
+
+// #!/usr/bin/env nextflow
+// nextflow.preview.dsl=2
+//
+// params.outdir = "."             // gets set in the nextflow.config files (to './results/trim_galore')
+// params.verbose = false
+// params.trim_galore_args = ''
+// // trim_galore_args are best passed into the workflow in the following manner, e.g.:
+// // --trim_galore_args="--clip_r1 10 --clip_r2 15 -j 2"
+//
+// if (params.verbose){
+//     println ("[WORKFLOW] TRIM GALORE ARGS: "      + params.trim_galore_args)
+// }
+//
+// // TODO: check the output files in some way
+// // include '../../../tests/functions/check_process_outputs.nf'
+// include '../main.nf'  // params (clip_r1: 6, clip_r2: 10) // how to pass additional parameters
+//
+// ch_read_files = Channel
+//   .fromFilePairs('../../../test-datasets/test*{1,2}.fastq.gz',size:-1)
+//   // .view()  // to check whether the input channel works
+//
+// workflow {
+//
+//     main:
+//         TRIM_GALORE (ch_read_files, params.outdir, params.trim_galore_args, params.verbose)
+//
+// }